diff --git a/ui/src/lib/agent-skills-state.test.ts b/ui/src/lib/agent-skills-state.test.ts
new file mode 100644
index 00000000..883ef860
--- /dev/null
+++ b/ui/src/lib/agent-skills-state.test.ts
@@ -0,0 +1,58 @@
+import { describe, expect, it } from "vitest";
+import { applyAgentSkillSnapshot } from "./agent-skills-state";
+
+describe("applyAgentSkillSnapshot", () => {
+  it("hydrates the initial snapshot without arming autosave", () => {
+    const result = applyAgentSkillSnapshot(
+      {
+        draft: [],
+        lastSaved: [],
+        hasHydratedSnapshot: false,
+      },
+      ["paperclip", "para-memory-files"],
+    );
+
+    expect(result).toEqual({
+      draft: ["paperclip", "para-memory-files"],
+      lastSaved: ["paperclip", "para-memory-files"],
+      hasHydratedSnapshot: true,
+      shouldSkipAutosave: true,
+    });
+  });
+
+  it("keeps unsaved local edits when a fresh snapshot arrives", () => {
+    const result = applyAgentSkillSnapshot(
+      {
+        draft: ["paperclip", "custom-skill"],
+        lastSaved: ["paperclip"],
+        hasHydratedSnapshot: true,
+      },
+      ["paperclip"],
+    );
+
+    expect(result).toEqual({
+      draft: ["paperclip", "custom-skill"],
+      lastSaved: ["paperclip"],
+      hasHydratedSnapshot: true,
+      shouldSkipAutosave: false,
+    });
+  });
+
+  it("adopts server state after a successful save and skips the follow-up autosave pass", () => {
+    const result = applyAgentSkillSnapshot(
+      {
+        draft: ["paperclip", "custom-skill"],
+        lastSaved: ["paperclip", "custom-skill"],
+        hasHydratedSnapshot: true,
+      },
+      ["paperclip", "custom-skill"],
+    );
+
+    expect(result).toEqual({
+      draft: ["paperclip", "custom-skill"],
+      lastSaved: ["paperclip", "custom-skill"],
+      hasHydratedSnapshot: true,
+      shouldSkipAutosave: true,
+    });
+  });
+});
diff --git a/ui/src/lib/agent-skills-state.ts b/ui/src/lib/agent-skills-state.ts
new file mode 100644
index 00000000..640b3819
--- /dev/null
+++ b/ui/src/lib/agent-skills-state.ts
@@ -0,0 +1,29 @@
+export interface AgentSkillDraftState {
+  draft: string[];
+  lastSaved: string[];
+  hasHydratedSnapshot: boolean;
+}
+
+export interface AgentSkillSnapshotApplyResult extends AgentSkillDraftState {
+  shouldSkipAutosave: boolean;
+}
+
+export function arraysEqual(a: string[], b: string[]): boolean {
+  if (a === b) return true;
+  if (a.length !== b.length) return false;
+  return a.every((value, index) => value === b[index]);
+}
+
+export function applyAgentSkillSnapshot(
+  state: AgentSkillDraftState,
+  desiredSkills: string[],
+): AgentSkillSnapshotApplyResult {
+  const shouldReplaceDraft = !state.hasHydratedSnapshot || arraysEqual(state.draft, state.lastSaved);
+
+  return {
+    draft: shouldReplaceDraft ? desiredSkills : state.draft,
+    lastSaved: desiredSkills,
+    hasHydratedSnapshot: true,
+    shouldSkipAutosave: shouldReplaceDraft,
+  };
+}
diff --git a/ui/src/pages/AgentDetail.tsx b/ui/src/pages/AgentDetail.tsx
index c891d6c3..1d020136 100644
--- a/ui/src/pages/AgentDetail.tsx
+++ b/ui/src/pages/AgentDetail.tsx
@@ -74,6 +74,7 @@ import {
 } from "@paperclipai/shared";
 import { redactHomePathUserSegments, redactHomePathUserSegmentsInValue } from "@paperclipai/adapter-utils";
 import { agentRouteRef } from "../lib/utils";
+import { applyAgentSkillSnapshot, arraysEqual } from "../lib/agent-skills-state";
 
 const runStatusIcons: Record<string, { icon: typeof CheckCircle2; color: string }> = {
   succeeded: { icon: CheckCircle2, color: "text-green-600 dark:text-green-400" },
@@ -137,12 +138,6 @@ const sourceLabels: Record<string, string> = {
 const LIVE_SCROLL_BOTTOM_TOLERANCE_PX = 32;
 type ScrollContainer = Window | HTMLElement;
 
-function arraysEqual(a: string[], b: string[]): boolean {
-  if (a === b) return true;
-  if (a.length !== b.length) return false;
-  return a.every((value, index) => value === b[index]);
-}
-
 function isWindowContainer(container: ScrollContainer): container is Window {
   return container === window;
 }
@@ -1250,6 +1245,8 @@ function AgentSkillsTab({
   const [skillDraft, setSkillDraft] = useState<string[]>([]);
   const [lastSavedSkills, setLastSavedSkills] = useState<string[]>([]);
   const lastSavedSkillsRef = useRef<string[]>([]);
+  const hasHydratedSkillSnapshotRef = useRef(false);
+  const skipNextSkillAutosaveRef = useRef(true);
 
   const { data: skillSnapshot, isLoading } = useQuery({
     queryKey: queryKeys.agents.skills(agent.id),
@@ -1277,16 +1274,36 @@ function AgentSkillsTab({
   });
 
   useEffect(() => {
-    if (!skillSnapshot) return;
-    setSkillDraft((current) =>
-      arraysEqual(current, lastSavedSkillsRef.current) ? skillSnapshot.desiredSkills : current,
-    );
-    lastSavedSkillsRef.current = skillSnapshot.desiredSkills;
-    setLastSavedSkills(skillSnapshot.desiredSkills);
-  }, [skillSnapshot]);
+    setSkillDraft([]);
+    setLastSavedSkills([]);
+    lastSavedSkillsRef.current = [];
+    hasHydratedSkillSnapshotRef.current = false;
+    skipNextSkillAutosaveRef.current = true;
+  }, [agent.id]);
 
   useEffect(() => {
     if (!skillSnapshot) return;
+    const nextState = applyAgentSkillSnapshot(
+      {
+        draft: skillDraft,
+        lastSaved: lastSavedSkillsRef.current,
+        hasHydratedSnapshot: hasHydratedSkillSnapshotRef.current,
+      },
+      skillSnapshot.desiredSkills,
+    );
+    skipNextSkillAutosaveRef.current = nextState.shouldSkipAutosave;
+    hasHydratedSkillSnapshotRef.current = nextState.hasHydratedSnapshot;
+    setSkillDraft(nextState.draft);
+    lastSavedSkillsRef.current = nextState.lastSaved;
+    setLastSavedSkills(nextState.lastSaved);
+  }, [skillDraft, skillSnapshot]);
+
+  useEffect(() => {
+    if (!skillSnapshot) return;
+    if (skipNextSkillAutosaveRef.current) {
+      skipNextSkillAutosaveRef.current = false;
+      return;
+    }
     if (syncSkills.isPending) return;
     if (arraysEqual(skillDraft, lastSavedSkillsRef.current)) return;
 
@@ -1409,7 +1426,7 @@ function AgentSkillsTab({
             const renderSkillRow = (skill: SkillRow) => {
               const adapterEntry = skill.adapterEntry ?? adapterEntryByName.get(skill.slug);
               const required = Boolean(adapterEntry?.required);
-              const checked = required || Boolean(adapterEntry?.desired) || skillDraft.includes(skill.slug);
+              const checked = required || skillDraft.includes(skill.slug);
               const disabled = required || skillSnapshot?.mode === "unsupported";
               const checkbox = (
                 <input