diff --git a/server/src/__tests__/agent-instructions-routes.test.ts b/server/src/__tests__/agent-instructions-routes.test.ts
index f35ef61060..6d36a820d3 100644
--- a/server/src/__tests__/agent-instructions-routes.test.ts
+++ b/server/src/__tests__/agent-instructions-routes.test.ts
@@ -328,6 +328,45 @@ describe("agent instructions bundle routes", () => {
     );
   });
 
+  it("preserves paperclip skill-sync selections when switching adapters", async () => {
+    // Desired skills live inside the per-adapter config under
+    // `paperclipSkillSync`, yet they are adapter-agnostic company-level
+    // selections. Switching adapter type must not silently wipe them — the
+    // server carries them over from the existing config the same way it
+    // preserves env/cwd and the instructions bundle.
+    mockAgentService.getById.mockResolvedValue({
+      ...makeAgent(),
+      adapterType: "claude_local",
+      adapterConfig: {
+        model: "claude-sonnet-4",
+        paperclipSkillSync: { desiredSkills: ["research", "code-review"] },
+      },
+    });
+
+    const res = await requestApp(await createApp(), (baseUrl) => request(baseUrl)
+      .patch("/api/agents/11111111-1111-4111-8111-111111111111?companyId=company-1")
+      .send({
+        adapterType: "codex_local",
+        replaceAdapterConfig: true,
+        adapterConfig: {
+          model: "gpt-5.4",
+        },
+      }));
+
+    expect(res.status, JSON.stringify(res.body)).toBe(200);
+    expect(mockAgentService.update).toHaveBeenCalledWith(
+      "11111111-1111-4111-8111-111111111111",
+      expect.objectContaining({
+        adapterType: "codex_local",
+        adapterConfig: expect.objectContaining({
+          model: "gpt-5.4",
+          paperclipSkillSync: { desiredSkills: ["research", "code-review"] },
+        }),
+      }),
+      expect.any(Object),
+    );
+  });
+
   it("merges same-adapter config patches so instructions metadata is not dropped", async () => {
     mockAgentService.getById.mockResolvedValue({
       ...makeAgent(),
diff --git a/server/src/routes/agents.ts b/server/src/routes/agents.ts
index e86851d871..1ac42fe9fa 100644
--- a/server/src/routes/agents.ts
+++ b/server/src/routes/agents.ts
@@ -2870,9 +2870,13 @@ export function agentRoutes(
         // Preserve adapter-agnostic keys (env, cwd, etc.) from the existing config
         // when the adapter type changes. Without this, a PATCH that includes
         // adapterConfig but omits these keys would silently drop them.
+        // `paperclipSkillSync` holds the agent's desired-skill selection, which is
+        // a company-level (adapter-agnostic) choice even though it is persisted
+        // inside the per-adapter config; switching adapters must not wipe it.
         const ADAPTER_AGNOSTIC_KEYS = [
           "env", "cwd", "timeoutSec", "graceSec",
           "promptTemplate", "bootstrapPromptTemplate",
+          "paperclipSkillSync",
         ] as const;
         for (const key of ADAPTER_AGNOSTIC_KEYS) {
           if (rawEffectiveAdapterConfig[key] === undefined && existingAdapterConfig[key] !== undefined) {
diff --git a/ui/src/lib/agent-config-patch.test.ts b/ui/src/lib/agent-config-patch.test.ts
index 7cdc79e2a2..46e6e85829 100644
--- a/ui/src/lib/agent-config-patch.test.ts
+++ b/ui/src/lib/agent-config-patch.test.ts
@@ -220,4 +220,28 @@ describe("buildAgentUpdatePatch", () => {
       replaceAdapterConfig: true,
     });
   });
+
+  it("preserves paperclip skill-sync selections when changing adapter types", () => {
+    // Desired skills are adapter-agnostic (company-level selections) but are
+    // persisted inside the per-adapter config under `paperclipSkillSync`. A
+    // patch that switches adapters must carry them over instead of wiping the
+    // agent's skills.
+    const agent = makeAgent();
+    agent.adapterConfig = {
+      ...agent.adapterConfig,
+      paperclipSkillSync: { desiredSkills: ["research", "code-review"] },
+    };
+
+    const patch = buildAgentUpdatePatch(
+      agent,
+      makeOverlay({
+        adapterType: "codex_local",
+        adapterConfig: { model: "gpt-5.4" },
+      }),
+    );
+
+    expect((patch.adapterConfig as Record<string, unknown>).paperclipSkillSync).toEqual({
+      desiredSkills: ["research", "code-review"],
+    });
+  });
 });
diff --git a/ui/src/lib/agent-config-patch.ts b/ui/src/lib/agent-config-patch.ts
index e57e0c05ab..325d8d8833 100644
--- a/ui/src/lib/agent-config-patch.ts
+++ b/ui/src/lib/agent-config-patch.ts
@@ -27,6 +27,10 @@ const ADAPTER_AGNOSTIC_KEYS = [
   "timeoutSec",
   "graceSec",
   "bootstrapPromptTemplate",
+  // Desired-skill selection is a company-level, adapter-agnostic choice even
+  // though it is persisted inside the per-adapter config; keep it when the
+  // adapter type changes so switching adapters does not wipe the agent's skills.
+  "paperclipSkillSync",
 ] as const;
 
 function omitUndefinedEntries(value: Record<string, unknown>) {