diff --git a/CONTEXT.md b/CONTEXT.md
index 2db04e7cf..7d7bbf046 100644
--- a/CONTEXT.md
+++ b/CONTEXT.md
@@ -107,7 +107,7 @@ _Avoid_: Configuration file (the wire format is not the in-memory or persisted s
 ## Flagged ambiguities
 
 - "Configuration" was used to mean both **Connection** and the bundled object (connection + schema + user preferences) — resolved: **Connection** is canonical, "Configuration" is legacy.
-- A Connection's data now has three distinct shapes that look similar but must not be conflated: the **Exported Connection File** (on-disk wire format), the in-memory configuration, and the IndexedDB storage shape. They are being separated into explicit types so each can evolve independently.
+- A Connection's data now has three distinct shapes that look similar but must not be conflated, each with its own explicit type: the **Exported Connection File** (`ExportedConnectionFile`, on-disk wire format), the in-memory merged configuration (`MergedConfiguration` — connection plus a live `Schema` with `lastUpdate` as a `Date`), and the persisted storage shape (`RawConfiguration` — connection only; the schema is stored separately in `schemaAtom`, never embedded). `mergeConfiguration` assembles a `MergedConfiguration` from a stored `RawConfiguration` and its active schema. Remaining work: `configurationAtom` still keys by `RawConfiguration`, to be migrated to a connection record.
 - "Node" means **Vertex** in code but is the preferred UI term for property graphs — resolved: use **Vertex** in code, "node" in UI copy.
 - "Attribute" vs "Property" — resolved: **Property** is canonical, "attribute" is legacy code term being phased out.
 - "Active connection" meant a single shared per-origin value, but the app consumed it as if it were per-tab — resolved: **Active Connection** is per-tab (sessionStorage), **Last Active Connection** is the shared persisted breadcrumb. The legacy `activeConfigurationAtom` / `active-configuration` key is reused as the breadcrumb.
diff --git a/packages/graph-explorer/src/core/ConfigurationProvider/types.test.ts b/packages/graph-explorer/src/core/ConfigurationProvider/types.test.ts
index ea97f3c1f..d0fb8e79e 100644
--- a/packages/graph-explorer/src/core/ConfigurationProvider/types.test.ts
+++ b/packages/graph-explorer/src/core/ConfigurationProvider/types.test.ts
@@ -60,15 +60,33 @@ describe("RawConfiguration", () => {
 
     expect(deserialized).toStrictEqual(configs);
   });
+});
 
-  test("serialization round-trip preserves configuration with schema", () => {
-    const config = createRandomRawConfiguration();
-    config.schema = createRandomSchema();
-
-    const serialized = serializeData(config);
-    const deserialized = deserializeData(serialized) as RawConfiguration;
-
-    expect(deserialized).toStrictEqual(config);
-    expect(deserialized.schema?.lastUpdate).toBeInstanceOf(Date);
+/**
+ * BACKWARD COMPATIBILITY — PERSISTED DATA
+ *
+ * `RawConfiguration` is persisted to IndexedDB via localforage. Older versions
+ * embedded the schema directly on the stored config (`RawConfiguration.schema`).
+ * That field has been removed — the schema now lives only in `schemaAtom` — but
+ * previously persisted configs may still carry it. This verifies that
+ * serialization round-trips such a legacy config losslessly, including reviving
+ * the embedded schema's `lastUpdate` back into a `Date`.
+ *
+ * DO NOT delete or weaken this test without confirming that legacy persisted
+ * configs carrying an embedded schema are no longer a concern.
+ */
+describe("backward compatibility: legacy embedded schema on stored configuration", () => {
+  test("serialization round-trip preserves a configuration carrying a legacy schema", () => {
+    // Use `as` to simulate the legacy shape that TypeScript no longer allows.
+    const legacyConfig = {
+      ...createRandomRawConfiguration(),
+      schema: createRandomSchema(),
+    } as RawConfiguration & { schema: SchemaStorageModel };
+
+    const serialized = serializeData(legacyConfig);
+    const deserialized = deserializeData(serialized) as typeof legacyConfig;
+
+    expect(deserialized).toStrictEqual(legacyConfig);
+    expect(deserialized.schema.lastUpdate).toBeInstanceOf(Date);
   });
 });
diff --git a/packages/graph-explorer/src/core/ConfigurationProvider/types.ts b/packages/graph-explorer/src/core/ConfigurationProvider/types.ts
index 1bea2321d..ab6695260 100644
--- a/packages/graph-explorer/src/core/ConfigurationProvider/types.ts
+++ b/packages/graph-explorer/src/core/ConfigurationProvider/types.ts
@@ -155,6 +155,11 @@ export function createEdgeConnection(options: {
   };
 }
 
+/**
+ * The persisted shape of a connection configuration, as stored in
+ * `configurationAtom` and IndexedDB. The schema is kept separately in
+ * `schemaAtom`, never embedded here.
+ */
 export type RawConfiguration = {
   /**
    * Unique identifier for this config
@@ -165,13 +170,25 @@ export type RawConfiguration = {
    * Connection configuration
    */
   connection?: ConnectionConfig;
+};
+
+/**
+ * A configuration assembled in memory by merging the stored
+ * {@link RawConfiguration} with its active schema and user styling. Unlike the
+ * persisted {@link RawConfiguration}, this carries the schema inline for the UI
+ * to consume.
+ */
+export type MergedConfiguration = RawConfiguration & {
   /**
    * Database schema: types, names, labels, icons, ...
+   *
+   * Always present — `mergeConfiguration` builds it from the active schema and
+   * user styling, defaulting to empty type lists when there is no schema yet.
    */
-  schema?: SchemaStorageModel;
+  schema: SchemaStorageModel;
 };
 
-export type ConfigurationContextProps = RawConfiguration & {
+export type ConfigurationContextProps = MergedConfiguration & {
   totalVertices: number;
   vertexTypes: Array<VertexType>;
   totalEdges: number;
diff --git a/packages/graph-explorer/src/core/ConfigurationProvider/useConfiguration.ts b/packages/graph-explorer/src/core/ConfigurationProvider/useConfiguration.ts
index 807a8b097..046d2ce38 100644
--- a/packages/graph-explorer/src/core/ConfigurationProvider/useConfiguration.ts
+++ b/packages/graph-explorer/src/core/ConfigurationProvider/useConfiguration.ts
@@ -19,16 +19,16 @@ const assembledConfigSelector = atom(get => {
   }
 
   const vertexTypesMap = new Set(
-    configuration.schema?.vertices.map(v => v.type),
+    configuration.schema.vertices.map(v => v.type),
   );
 
-  const edgeTypesMap = new Set(configuration.schema?.edges.map(e => e.type));
+  const edgeTypesMap = new Set(configuration.schema.edges.map(e => e.type));
 
   const result: ConfigurationContextProps = {
     ...configuration,
-    totalVertices: configuration.schema?.totalVertices ?? 0,
+    totalVertices: configuration.schema.totalVertices ?? 0,
     vertexTypes: vertexTypesMap.keys().toArray(),
-    totalEdges: configuration.schema?.totalEdges ?? 0,
+    totalEdges: configuration.schema.totalEdges ?? 0,
     edgeTypes: edgeTypesMap.keys().toArray(),
   };
   return result;
diff --git a/packages/graph-explorer/src/core/StateProvider/configuration.test.ts b/packages/graph-explorer/src/core/StateProvider/configuration.test.ts
index a42e7b6d5..bb0fadad1 100644
--- a/packages/graph-explorer/src/core/StateProvider/configuration.test.ts
+++ b/packages/graph-explorer/src/core/StateProvider/configuration.test.ts
@@ -14,6 +14,7 @@ import {
 } from "@/utils/testing";
 
 import type {
+  MergedConfiguration,
   RawConfiguration,
   VertexTypeConfig,
 } from "../ConfigurationProvider";
@@ -73,7 +74,7 @@ describe("mergedConfiguration", () => {
         totalEdges: 0,
         totalVertices: 0,
       },
-    } satisfies RawConfiguration);
+    } satisfies MergedConfiguration);
   });
 
   it("should use schema when provided", () => {
@@ -114,7 +115,7 @@ describe("mergedConfiguration", () => {
         graphDbUrl: config.connection?.graphDbUrl ?? "",
       },
       schema: expectedSchema,
-    } satisfies RawConfiguration);
+    } satisfies MergedConfiguration);
   });
 
   it("should use styling when provided", () => {
@@ -289,6 +290,32 @@ describe("mergedConfiguration", () => {
       RESERVED_TYPES_PROPERTY,
     );
   });
+
+  it("should ignore a schema embedded on the stored config and use the active schema", () => {
+    // A legacy stored config may carry an embedded schema (the field that was
+    // removed from RawConfiguration). The merge must source its schema solely
+    // from the active schema argument, never from the stored config.
+    const staleVertex = createRandomVertexTypeConfig();
+    staleVertex.type = createVertexType("StaleType");
+    const staleSchema = createRandomSchema();
+    staleSchema.vertices = [staleVertex];
+
+    const config = {
+      ...createRandomRawConfiguration(),
+      schema: staleSchema,
+    } as RawConfiguration & { schema: SchemaStorageModel };
+
+    const activeVertex = createRandomVertexTypeConfig();
+    activeVertex.type = createVertexType("ActiveType");
+    const activeSchema = createRandomSchema();
+    activeSchema.vertices = [activeVertex];
+
+    const result = mergeConfiguration(activeSchema, config, {});
+
+    expect(result.schema.vertices.map(v => v.type)).toEqual([
+      createVertexType("ActiveType"),
+    ]);
+  });
 });
 
 /** Sorts the configs by type name */
diff --git a/packages/graph-explorer/src/core/StateProvider/configuration.ts b/packages/graph-explorer/src/core/StateProvider/configuration.ts
index 46bfdaf7e..a255613fb 100644
--- a/packages/graph-explorer/src/core/StateProvider/configuration.ts
+++ b/packages/graph-explorer/src/core/StateProvider/configuration.ts
@@ -10,6 +10,7 @@ import {
   configurationAtom,
   type EdgeType,
   type EdgeTypeConfig,
+  type MergedConfiguration,
   type RawConfiguration,
   userStylingAtom,
   type VertexType,
@@ -61,7 +62,7 @@ export function mergeConfiguration(
   currentSchema: SchemaStorageModel | null | undefined,
   currentConfig: RawConfiguration,
   userStyling: UserStyling,
-): RawConfiguration {
+): MergedConfiguration {
   const prefsVertexMap = toMapByType(userStyling.vertices);
   const mergedVertices = (currentSchema?.vertices ?? [])
     .map(schemaVertex =>
@@ -153,22 +154,22 @@ const mergeEdge = (
 
 export const allVertexTypeConfigsSelector = atom(get => {
   const configuration = get(mergedConfigurationSelector);
-  return new Map(configuration?.schema?.vertices.map(vt => [vt.type, vt]));
+  return new Map(configuration?.schema.vertices.map(vt => [vt.type, vt]));
 });
 
 export const allEdgeTypeConfigsSelector = atom(get => {
   const configuration = get(mergedConfigurationSelector);
-  return new Map(configuration?.schema?.edges.map(et => [et.type, et]));
+  return new Map(configuration?.schema.edges.map(et => [et.type, et]));
 });
 
 export const vertexTypesSelector = atom(get => {
   const configuration = get(mergedConfigurationSelector);
-  return configuration?.schema?.vertices?.map(vt => vt.type) || [];
+  return configuration?.schema.vertices.map(vt => vt.type) || [];
 });
 
 export const edgeTypesSelector = atom(get => {
   const configuration = get(mergedConfigurationSelector);
-  return configuration?.schema?.edges?.map(vt => vt.type) || [];
+  return configuration?.schema.edges.map(vt => vt.type) || [];
 });
 
 export const defaultVertexTypeConfig = {
diff --git a/packages/graph-explorer/src/core/StateProvider/localDb.test.ts b/packages/graph-explorer/src/core/StateProvider/localDb.test.ts
index a8634e4e7..e6b5bcb1d 100644
--- a/packages/graph-explorer/src/core/StateProvider/localDb.test.ts
+++ b/packages/graph-explorer/src/core/StateProvider/localDb.test.ts
@@ -5,12 +5,16 @@ import {
   createRandomName,
 } from "@shared/utils/testing";
 
+import type { RawConfiguration } from "@/core";
+
 import { toJsonFileData } from "@/utils/fileData";
 import {
   createRandomRawConfiguration,
   createRandomSchema,
 } from "@/utils/testing";
 
+import type { SchemaStorageModel } from "./schema";
+
 import {
   addRestoredPrefix,
   createBackupData,
@@ -209,11 +213,14 @@ describe("backward compatibility: legacy schema field on stored configuration",
     const localDb = createFakeLocalDb();
 
     // A stored config in the legacy shape: the schema is duplicated onto the
-    // RawConfiguration itself, which TypeScript still allows but no current
-    // writer produces.
+    // RawConfiguration itself. The current type no longer declares `schema`, so
+    // we cast to attach it — simulating a stale IndexedDB blob written by an
+    // older version.
     const config = createRandomRawConfiguration();
     const schema = createRandomSchema();
-    const legacyConfig = { ...config, schema } as typeof config;
+    const legacyConfig = { ...config, schema } as RawConfiguration & {
+      schema: SchemaStorageModel;
+    };
 
     const configMap = new Map([[config.id, legacyConfig]]);
     const schemaMap = new Map([[config.id, schema]]);
diff --git a/packages/graph-explorer/src/modules/AvailableConnections/useImportConnectionFile.test.tsx b/packages/graph-explorer/src/modules/AvailableConnections/useImportConnectionFile.test.tsx
index 29acfc5c7..81277480e 100644
--- a/packages/graph-explorer/src/modules/AvailableConnections/useImportConnectionFile.test.tsx
+++ b/packages/graph-explorer/src/modules/AvailableConnections/useImportConnectionFile.test.tsx
@@ -533,9 +533,9 @@ describe("backward compatibility: legacy exported connection file with embedded
     );
 
     // The schema must NOT be stored on the config entry — it belongs in
-    // schemaAtom. This is the invariant the dead `RawConfiguration.schema`
-    // merge leg relies on staying true.
-    expect(importedConfig.schema).toBeUndefined();
+    // schemaAtom. `RawConfiguration` no longer declares a `schema` field, so we
+    // probe for a stray one to prove import never writes it back.
+    expect((importedConfig as { schema?: unknown }).schema).toBeUndefined();
 
     // The full schema is split out into schemaAtom, styling and all.
     expect(importedSchema.vertices.map(v => v.type)).toStrictEqual([
diff --git a/packages/graph-explorer/src/utils/saveConfigurationToFile.test.ts b/packages/graph-explorer/src/utils/saveConfigurationToFile.test.ts
index 4c6bcce1b..3db288bb8 100644
--- a/packages/graph-explorer/src/utils/saveConfigurationToFile.test.ts
+++ b/packages/graph-explorer/src/utils/saveConfigurationToFile.test.ts
@@ -17,15 +17,27 @@ vi.mock("file-saver", () => ({
 
 const saveAsMock = vi.mocked(fileSaver.saveAs);
 
+/**
+ * Builds a merged configuration for export tests. Defaults to an empty schema
+ * and zeroed runtime counts; pass overrides to exercise specific cases.
+ */
+function makeConfig(
+  overrides: Partial<ConfigurationContextProps> = {},
+): ConfigurationContextProps {
+  return {
+    ...createRandomRawConfiguration(),
+    schema: { vertices: [], edges: [] },
+    totalVertices: 0,
+    vertexTypes: [],
+    totalEdges: 0,
+    edgeTypes: [],
+    ...overrides,
+  };
+}
+
 describe("saveConfigurationToFile", () => {
   it("should save a minimal configuration to file", () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    const config = makeConfig();
 
     saveConfigurationToFile(config);
 
@@ -38,14 +50,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should use id as displayLabel if displayLabel is not provided", () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
-      displayLabel: undefined,
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    const config = makeConfig({ displayLabel: undefined });
 
     saveConfigurationToFile(config);
 
@@ -54,16 +59,11 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should include connection with default queryEngine if not provided", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       connection: {
         url: "https://example.com",
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -76,17 +76,12 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should preserve existing queryEngine", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       connection: {
         url: "https://example.com",
         queryEngine: "sparql",
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -98,8 +93,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should export schema with vertices and edges", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       schema: {
         vertices: [
           {
@@ -130,7 +124,7 @@ describe("saveConfigurationToFile", () => {
       vertexTypes: [createVertexType("Person"), createVertexType("Company")],
       totalEdges: 50,
       edgeTypes: [createEdgeType("worksAt")],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -149,8 +143,7 @@ describe("saveConfigurationToFile", () => {
     // it (an explicit toISOString or a Date flushed by JSON.stringify), so the
     // writer's lastUpdate type can change without altering the file.
     const lastUpdate = new Date("2024-01-01T12:30:00Z");
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       schema: {
         vertices: [],
         edges: [],
@@ -160,11 +153,7 @@ describe("saveConfigurationToFile", () => {
         lastUpdate,
         lastSyncFail: false,
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -176,8 +165,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should export prefixes without internal properties", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       schema: {
         vertices: [],
         edges: [],
@@ -196,11 +184,7 @@ describe("saveConfigurationToFile", () => {
         lastUpdate: new Date(),
         lastSyncFail: false,
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -221,14 +205,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should handle empty schema", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
-      schema: undefined,
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    const config = makeConfig();
 
     saveConfigurationToFile(config);
 
@@ -243,14 +220,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should handle missing connection", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
-      connection: undefined,
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    const config = makeConfig({ connection: undefined });
 
     saveConfigurationToFile(config);
 
@@ -271,13 +241,12 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should only export necessary fields", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       totalVertices: 100,
       vertexTypes: [createVertexType("Person")],
       totalEdges: 50,
       edgeTypes: [createEdgeType("knows")],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -299,8 +268,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should produce a file that passes import validation", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       connection: {
         url: "https://neptune.example.com:8182",
         queryEngine: "gremlin",
@@ -330,7 +298,7 @@ describe("saveConfigurationToFile", () => {
       vertexTypes: [createVertexType("Person")],
       totalEdges: 1,
       edgeTypes: [createEdgeType("knows")],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -355,8 +323,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should export edgeConnections when present", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       schema: {
         vertices: [],
         edges: [],
@@ -379,11 +346,7 @@ describe("saveConfigurationToFile", () => {
           },
         ],
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
@@ -407,8 +370,7 @@ describe("saveConfigurationToFile", () => {
   });
 
   it("should handle undefined edgeConnections", async () => {
-    const config: ConfigurationContextProps = {
-      ...createRandomRawConfiguration(),
+    const config = makeConfig({
       schema: {
         vertices: [],
         edges: [],
@@ -419,11 +381,7 @@ describe("saveConfigurationToFile", () => {
         lastSyncFail: false,
         edgeConnections: undefined,
       },
-      totalVertices: 0,
-      vertexTypes: [],
-      totalEdges: 0,
-      edgeTypes: [],
-    };
+    });
 
     saveConfigurationToFile(config);
 
diff --git a/packages/graph-explorer/src/utils/saveConfigurationToFile.ts b/packages/graph-explorer/src/utils/saveConfigurationToFile.ts
index 88b6f569e..978265c5a 100644
--- a/packages/graph-explorer/src/utils/saveConfigurationToFile.ts
+++ b/packages/graph-explorer/src/utils/saveConfigurationToFile.ts
@@ -16,11 +16,11 @@ const saveConfigurationToFile = (config: ConfigurationContextProps) => {
       queryEngine: config.connection?.queryEngine || "gremlin",
     },
     schema: {
-      vertices: config.schema?.vertices || [],
-      edges: config.schema?.edges || [],
-      prefixes: config.schema?.prefixes,
-      lastUpdate: config.schema?.lastUpdate,
-      edgeConnections: config.schema?.edgeConnections,
+      vertices: config.schema.vertices,
+      edges: config.schema.edges,
+      prefixes: config.schema.prefixes,
+      lastUpdate: config.schema.lastUpdate,
+      edgeConnections: config.schema.edgeConnections,
     },
   };
 
diff --git a/packages/graph-explorer/src/utils/testing/DbState.ts b/packages/graph-explorer/src/utils/testing/DbState.ts
index 3f61a9bc7..1ea058c55 100644
--- a/packages/graph-explorer/src/utils/testing/DbState.ts
+++ b/packages/graph-explorer/src/utils/testing/DbState.ts
@@ -63,9 +63,7 @@ export class DbState {
   constructor(explorer: Explorer = createMockExplorer()) {
     this.#activeSchema = createRandomSchema();
 
-    const config = createRandomRawConfiguration();
-    config.schema = this.#activeSchema;
-    this.activeConfig = config;
+    this.activeConfig = createRandomRawConfiguration();
 
     this.activeStyling = createRandomUserStyling();