diff --git a/api/server/services/Endpoints/agents/initialize.js b/api/server/services/Endpoints/agents/initialize.js
index 1666d2a556..5270fd821f 100644
--- a/api/server/services/Endpoints/agents/initialize.js
+++ b/api/server/services/Endpoints/agents/initialize.js
@@ -202,7 +202,7 @@ const initializeClient = async ({ req, res, signal, endpointOption }) => {
   const enabledCapabilities = new Set(appConfig?.endpoints?.[EModelEndpoint.agents]?.capabilities);
   const ephemeralSkillsToggle = req.body?.ephemeralAgent?.skills;
   const skillsCapabilityEnabled =
-    enabledCapabilities.has(AgentCapabilities.skills) && ephemeralSkillsToggle !== false;
+    enabledCapabilities.has(AgentCapabilities.skills) && ephemeralSkillsToggle === true;
   const accessibleSkillIds = skillsCapabilityEnabled
     ? await findAccessibleResources({
         userId: req.user.id,
diff --git a/packages/api/src/agents/skillFiles.ts b/packages/api/src/agents/skillFiles.ts
index 2954b94111..80a6055e16 100644
--- a/packages/api/src/agents/skillFiles.ts
+++ b/packages/api/src/agents/skillFiles.ts
@@ -88,16 +88,17 @@ export async function primeSkillFiles(
           const files: PrimeSkillFilesResult['files'] = [];
           const sessionId = firstWithId.codeEnvIdentifier.split('/')[0];
 
-          // SKILL.md doesn't have a codeEnvIdentifier; find it by name convention
-          // (it was uploaded with the batch and shares the session)
-          for (const sf of skillFiles) {
-            if (sf.codeEnvIdentifier) {
-              const [sid, fid] = sf.codeEnvIdentifier.split('/');
+          // All files must have identifiers for the cache to be complete.
+          // Any missing identifier means partial persistence — fall through to re-upload.
+          const allHaveIds = skillFiles.every((sf) => sf.codeEnvIdentifier);
+          if (allHaveIds) {
+            for (const sf of skillFiles) {
+              const [sid, fid] = (sf.codeEnvIdentifier as string).split('/');
               files.push({ id: fid, session_id: sid, name: `${skill.name}/${sf.relativePath}` });
             }
           }
 
-          if (files.length > 0) {
+          if (allHaveIds && files.length > 0) {
             logger.debug(
               `[primeSkillFiles] Session still active for skill "${skill.name}", reusing ${files.length} files`,
             );
@@ -282,11 +283,11 @@ export async function primeInvokedSkills(
     // ALL distinct sessions for freshness. If all are active, return cached
     // references with zero re-uploads. If any expired, re-upload everything.
     if (deps.getSessionInfo && deps.checkIfActive) {
-      const allFilesWithIds = fileListResults
-        .flatMap((r) => r.files)
-        .filter((f) => f.codeEnvIdentifier);
+      const allFiles = fileListResults.flatMap((r) => r.files);
+      const allFilesWithIds = allFiles.filter((f) => f.codeEnvIdentifier);
 
-      if (allFilesWithIds.length > 0) {
+      // Only use cache when ALL files have identifiers (no partial persistence)
+      if (allFilesWithIds.length > 0 && allFilesWithIds.length === allFiles.length) {
         const sessionIds = new Set(allFilesWithIds.map((f) => f.codeEnvIdentifier!.split('/')[0]));
 
         const checkResults = await Promise.all(