diff --git a/packages/adapter-utils/src/server-utils.ts b/packages/adapter-utils/src/server-utils.ts
index 3b79636f..ba35807a 100644
--- a/packages/adapter-utils/src/server-utils.ts
+++ b/packages/adapter-utils/src/server-utils.ts
@@ -391,9 +391,32 @@ export function readPaperclipSkillSyncPreference(config: Record<string, unknown>
   };
 }
 
+function canonicalizeDesiredPaperclipSkillReference(
+  reference: string,
+  availableEntries: Array<{ key: string; runtimeName?: string | null }>,
+): string {
+  const normalizedReference = reference.trim().toLowerCase();
+  if (!normalizedReference) return "";
+
+  const exactKey = availableEntries.find((entry) => entry.key.trim().toLowerCase() === normalizedReference);
+  if (exactKey) return exactKey.key;
+
+  const byRuntimeName = availableEntries.filter((entry) =>
+    typeof entry.runtimeName === "string" && entry.runtimeName.trim().toLowerCase() === normalizedReference,
+  );
+  if (byRuntimeName.length === 1) return byRuntimeName[0]!.key;
+
+  const slugMatches = availableEntries.filter((entry) =>
+    entry.key.trim().toLowerCase().split("/").pop() === normalizedReference,
+  );
+  if (slugMatches.length === 1) return slugMatches[0]!.key;
+
+  return normalizedReference;
+}
+
 export function resolvePaperclipDesiredSkillNames(
   config: Record<string, unknown>,
-  availableEntries: Array<{ key: string; required?: boolean }>,
+  availableEntries: Array<{ key: string; runtimeName?: string | null; required?: boolean }>,
 ): string[] {
   const preference = readPaperclipSkillSyncPreference(config);
   const requiredSkills = availableEntries
@@ -402,7 +425,10 @@ export function resolvePaperclipDesiredSkillNames(
   if (!preference.explicit) {
     return Array.from(new Set(requiredSkills));
   }
-  return Array.from(new Set([...requiredSkills, ...preference.desiredSkills]));
+  const desiredSkills = preference.desiredSkills
+    .map((reference) => canonicalizeDesiredPaperclipSkillReference(reference, availableEntries))
+    .filter(Boolean);
+  return Array.from(new Set([...requiredSkills, ...desiredSkills]));
 }
 
 export function writePaperclipSkillSyncPreference(
diff --git a/server/src/__tests__/claude-local-skill-sync.test.ts b/server/src/__tests__/claude-local-skill-sync.test.ts
index a103aa7c..b8b761b2 100644
--- a/server/src/__tests__/claude-local-skill-sync.test.ts
+++ b/server/src/__tests__/claude-local-skill-sync.test.ts
@@ -39,4 +39,23 @@ describe("claude local skill sync", () => {
     expect(snapshot.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("configured");
     expect(snapshot.entries.find((entry) => entry.key === createAgentKey)?.state).toBe("configured");
   });
+
+  it("normalizes legacy flat Paperclip skill refs to canonical keys", async () => {
+    const snapshot = await listClaudeSkills({
+      agentId: "agent-3",
+      companyId: "company-1",
+      adapterType: "claude_local",
+      config: {
+        paperclipSkillSync: {
+          desiredSkills: ["paperclip"],
+        },
+      },
+    });
+
+    expect(snapshot.warnings).toEqual([]);
+    expect(snapshot.desiredSkills).toContain(paperclipKey);
+    expect(snapshot.desiredSkills).not.toContain("paperclip");
+    expect(snapshot.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("configured");
+    expect(snapshot.entries.find((entry) => entry.key === "paperclip")).toBeUndefined();
+  });
 });
diff --git a/server/src/__tests__/codex-local-skill-sync.test.ts b/server/src/__tests__/codex-local-skill-sync.test.ts
index 7068e43f..a78d37e7 100644
--- a/server/src/__tests__/codex-local-skill-sync.test.ts
+++ b/server/src/__tests__/codex-local-skill-sync.test.ts
@@ -86,4 +86,29 @@ describe("codex local skill sync", () => {
     expect(after.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("installed");
     expect((await fs.lstat(path.join(codexHome, "skills", "paperclip"))).isSymbolicLink()).toBe(true);
   });
+
+  it("normalizes legacy flat Paperclip skill refs before reporting persistent state", async () => {
+    const codexHome = await makeTempDir("paperclip-codex-legacy-skill-sync-");
+    cleanupDirs.add(codexHome);
+
+    const snapshot = await listCodexSkills({
+      agentId: "agent-3",
+      companyId: "company-1",
+      adapterType: "codex_local",
+      config: {
+        env: {
+          CODEX_HOME: codexHome,
+        },
+        paperclipSkillSync: {
+          desiredSkills: ["paperclip"],
+        },
+      },
+    });
+
+    expect(snapshot.warnings).toEqual([]);
+    expect(snapshot.desiredSkills).toContain(paperclipKey);
+    expect(snapshot.desiredSkills).not.toContain("paperclip");
+    expect(snapshot.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("missing");
+    expect(snapshot.entries.find((entry) => entry.key === "paperclip")).toBeUndefined();
+  });
 });