diff --git a/server/src/services/agent-instructions.ts b/server/src/services/agent-instructions.ts
index 231ed839..6dcbb38f 100644
--- a/server/src/services/agent-instructions.ts
+++ b/server/src/services/agent-instructions.ts
@@ -9,6 +9,7 @@ const ROOT_KEY = "instructionsRootPath";
 const ENTRY_KEY = "instructionsEntryFile";
 const FILE_KEY = "instructionsFilePath";
 const PROMPT_KEY = "promptTemplate";
+/** @deprecated Use the managed instructions bundle system instead. */
 const BOOTSTRAP_PROMPT_KEY = "bootstrapPromptTemplate";
 const LEGACY_PROMPT_TEMPLATE_PATH = "promptTemplate.legacy.md";
 const IGNORED_INSTRUCTIONS_FILE_NAMES = new Set([".DS_Store", "Thumbs.db", "Desktop.ini"]);
diff --git a/server/src/services/company-portability.ts b/server/src/services/company-portability.ts
index 7cfe8ffa..db4be18a 100644
--- a/server/src/services/company-portability.ts
+++ b/server/src/services/company-portability.ts
@@ -1475,7 +1475,7 @@ function normalizePortableConfig(
       key === "instructionsRootPath" ||
       key === "instructionsEntryFile" ||
       key === "promptTemplate" ||
-      key === "bootstrapPromptTemplate" ||
+      key === "bootstrapPromptTemplate" || // deprecated — kept for backward compat
       key === "paperclipSkillSync"
     ) continue;
     if (key === "env") continue;
@@ -3895,7 +3895,7 @@ export function companyPortabilityService(db: Db, storage?: StorageService) {
           desiredSkills,
         );
         delete adapterConfigWithSkills.promptTemplate;
-        delete adapterConfigWithSkills.bootstrapPromptTemplate;
+        delete adapterConfigWithSkills.bootstrapPromptTemplate; // deprecated
         delete adapterConfigWithSkills.instructionsFilePath;
         delete adapterConfigWithSkills.instructionsBundleMode;
         delete adapterConfigWithSkills.instructionsRootPath;