diff --git a/api/server/services/Endpoints/agents/initialize.js b/api/server/services/Endpoints/agents/initialize.js
index 01b97e97a9..2367f58440 100644
--- a/api/server/services/Endpoints/agents/initialize.js
+++ b/api/server/services/Endpoints/agents/initialize.js
@@ -295,11 +295,22 @@ const initializeClient = async ({ req, res, signal, endpointOption }) => {
       if (!ctx.tool_resources) {
         ctx.tool_resources = {};
       }
-      const addProvisionedFile = (file, resourceType) => {
+      const addProvisionedFile = (file, resourceType, agentScoped) => {
         if (!file.file_id) {
           return;
         }
         const resource = ctx.tool_resources[resourceType] ?? {};
+        /** Agent-scoped file_search files are embedded under `entity_id: agentId`, so
+         *  they must be queried by `file_ids` (primeFiles marks those `fromAgent` and
+         *  passes `entity_id`); user chat attachments and code files live in `files`. */
+        if (agentScoped && resourceType === EToolResources.file_search) {
+          const fileIds = resource.file_ids ? [...resource.file_ids] : [];
+          if (!fileIds.includes(file.file_id)) {
+            fileIds.push(file.file_id);
+          }
+          ctx.tool_resources[resourceType] = { ...resource, file_ids: fileIds };
+          return;
+        }
         const files = resource.files ? [...resource.files] : [];
         if (!files.some((existing) => existing.file_id === file.file_id)) {
           files.push(file);
@@ -341,7 +352,11 @@ const initializeClient = async ({ req, res, signal, endpointOption }) => {
             });
             if (result.embedded) {
               file.embedded = true;
-              addProvisionedFile(file, EToolResources.file_search);
+              addProvisionedFile(
+                file,
+                EToolResources.file_search,
+                entityIdForFile(file) !== undefined,
+              );
               if (result.fileUpdate) {
                 pendingUpdates.push(result.fileUpdate);
               }
diff --git a/packages/data-provider/src/codeEnvRef.ts b/packages/data-provider/src/codeEnvRef.ts
index 81187ff78f..fa66368f6f 100644
--- a/packages/data-provider/src/codeEnvRef.ts
+++ b/packages/data-provider/src/codeEnvRef.ts
@@ -51,6 +51,9 @@ interface CodeEnvRefBase {
   id: string;
   storage_session_id: string;
   file_id: string;
+  /** Epoch ms when the file was uploaded to the code env; drives the liveness
+   *  fast-path (distinct from the usage-bumped `updatedAt`). */
+  provisionedAt?: number;
 }
 
 export type CodeEnvRef =
diff --git a/packages/data-schemas/src/schema/file.ts b/packages/data-schemas/src/schema/file.ts
index 1742e503f7..1ae004aae3 100644
--- a/packages/data-schemas/src/schema/file.ts
+++ b/packages/data-schemas/src/schema/file.ts
@@ -130,6 +130,7 @@ const file: Schema<IMongoFile> = new Schema(
             storage_session_id: { type: String, required: true },
             file_id: { type: String, required: true },
             version: { type: Number },
+            provisionedAt: { type: Number },
           },
           { _id: false },
         ),