diff --git a/src/main/services/builtin-skills.ts b/src/main/services/builtin-skills.ts
index 137c0b2a..09e3cbeb 100644
--- a/src/main/services/builtin-skills.ts
+++ b/src/main/services/builtin-skills.ts
@@ -80,7 +80,7 @@ export function stageBuiltinSkillsLibrary(sourceRoot: string, libraryRoot: strin
  * the org does not carry yet, restores retired skills the bundle ships again,
  * upgrades skills whose files changed (moving bindings onto the new
  * revision), then retires active skills whose slug the bundle no longer
- * ships. Retired skills leave list_skills and stop being grantable.
+ * ships. Retired skills leave list_skills, stop being grantable, and stop loading into runs.
  */
 export function importStagedSkills(skills: SkillService, orgId: string, staged: StagedBuiltinSkill[]): BuiltinSkillSyncReport {
   const report: BuiltinSkillSyncReport = { imported: 0, upgraded: 0, restored: 0, skipped: 0, retired: 0, failures: [] };
diff --git a/src/main/services/skill-service.ts b/src/main/services/skill-service.ts
index 0d3c0019..50096de4 100644
--- a/src/main/services/skill-service.ts
+++ b/src/main/services/skill-service.ts
@@ -57,9 +57,9 @@ export class SkillService {
 
   /**
    * Retires every active skill whose slug is not in `keepSlugs`, so the org
-   * catalogue mirrors the shipped bundle. Bindings pin revisions directly
-   * and keep resolving; retired skills leave list_skills and cannot be
-   * granted anew. Returns the retired slugs.
+   * catalogue mirrors the shipped bundle. Retired skills leave list_skills,
+   * cannot be granted, and stop loading into runs; their bindings stay so a
+   * restore brings them back. Returns the retired slugs.
    */
   retireSkillsNotIn(orgId: string, keepSlugs: string[]): string[] {
     const keep = new Set(keepSlugs);
@@ -245,9 +245,10 @@ export class SkillService {
    */
   hasRuntimeSkills(orgId: string, agentId: string): boolean {
     if (this.forcedSkillRows(orgId).length > 0) return true;
-    return Boolean(this.db.prepare(
-      "select id from skill_bindings where org_id = ? and agent_id = ? and enabled = 1 limit 1",
-    ).get(orgId, agentId));
+    return Boolean(this.db.prepare(`
+      select sb.id from skill_bindings sb join skill_definitions sd on sd.id = sb.skill_id and sd.status = 'active'
+      where sb.org_id = ? and sb.agent_id = ? and sb.enabled = 1 limit 1
+    `).get(orgId, agentId));
   }
 
   /**
@@ -279,6 +280,14 @@ export class SkillService {
     return [];
   }
 
+  private carriesRetiredSkill(revisionIds: string[]): boolean {
+    if (revisionIds.length === 0) return false;
+    return Boolean(this.db.prepare(`
+      select 1 from skill_revisions sr join skill_definitions sd on sd.id = sr.skill_id
+      where sd.status <> 'active' and sr.id in (${revisionIds.map(() => "?").join(", ")}) limit 1
+    `).get(...revisionIds));
+  }
+
   private appLanguage(): string {
     const row = this.db.prepare("select language from app_state where id = 1").get() as { language: string } | undefined;
     return row?.language === "zh" ? "zh" : "en";
@@ -292,12 +301,13 @@ export class SkillService {
    * prompt instead of silently overflowing the model's context.
    */
   resolveRuntimeSnapshot(input: ResolveAgentSkillsInput): string {
-    // Idempotent per run: a run interrupted after resolving (crash, quit) is
-    // re-queued by startup recovery and must reuse its frozen skill set, not
-    // die on a uniqueness error that burns real retry budget.
-    const existingSnapshot = this.db.prepare("select id from skill_runtime_snapshots where agent_id = ? and run_id = ?")
-      .get(input.agentId, input.runId) as { id: string } | undefined;
-    if (existingSnapshot) return existingSnapshot.id;
+    // Idempotent per run: a re-queued run reuses its frozen skill set unless a skill in it was retired since.
+    const existingSnapshot = this.db.prepare("select id, source_revision_ids from skill_runtime_snapshots where agent_id = ? and run_id = ?")
+      .get(input.agentId, input.runId) as { id: string; source_revision_ids: string } | undefined;
+    if (existingSnapshot) {
+      if (!this.carriesRetiredSkill(JSON.parse(existingSnapshot.source_revision_ids) as string[])) return existingSnapshot.id;
+      this.db.prepare("delete from skill_runtime_snapshots where id = ?").run(existingSnapshot.id);
+    }
     const forcedRows = this.forcedSkillRows(input.orgId);
     const boundRows = this.db.prepare(`
       select
@@ -307,6 +317,7 @@ export class SkillService {
         sr.manifest_json,
         sa.object_key
       from skill_bindings sb
+      join skill_definitions sd on sd.id = sb.skill_id and sd.status = 'active'
       join skill_revisions sr on sr.id = sb.pinned_revision_id
       join skill_artifacts sa on sa.revision_id = sr.id and sa.artifact_type in ('entrypoint', 'markdown')
       where sb.org_id = ? and sb.agent_id = ? and sb.enabled = 1
diff --git a/tests/unit/builtin-skills.test.ts b/tests/unit/builtin-skills.test.ts
index a1ecc900..5128373b 100644
--- a/tests/unit/builtin-skills.test.ts
+++ b/tests/unit/builtin-skills.test.ts
@@ -154,22 +154,45 @@ describe("built-in skills", () => {
     h.connection.close();
   });
 
-  test("a skill the bundle drops and later ships again comes back active", () => {
+  test("a skill the bundle drops stops applying to bound agents, and comes back when shipped again", () => {
     const h = harness();
     const sync = () => h.connection.transaction(() => importStagedSkills(h.skills, h.orgId, stageBuiltinSkillsLibrary(h.sourceRoot, h.libraryRoot)));
     sync();
+    const skill = h.connection.db.prepare(`
+      select sd.id, sr.id as revision_id from skill_definitions sd join skill_revisions sr on sr.skill_id = sd.id
+      where sd.org_id = ? and sd.slug = 'engineering-backend-architect'
+    `).get(h.orgId) as { id: string; revision_id: string };
+    let agentId = "";
+    h.connection.transaction(() => {
+      agentId = h.organization.createAgent({
+        orgId: h.orgId, name: "Ada", role: "Engineer", department: "Engineering",
+        modelProviderId: null, modelId: null, budgetCents: 1000, managerAgentId: null,
+      });
+      h.skills.bind({ orgId: h.orgId, agentId, skillId: skill.id, revisionId: skill.revision_id });
+    });
+    const prompt = (runId: string) => {
+      const id = h.connection.transaction(() => h.skills.resolveRuntimeSnapshot({ orgId: h.orgId, agentId, runId, maxTokens: SKILL_TOKENS, taskText: "" }));
+      return (h.connection.db.prepare("select compiled_prompt from skill_runtime_snapshots where id = ?").get(id) as { compiled_prompt: string }).compiled_prompt;
+    };
+    expect(prompt("run_before")).toContain("# Skill: Backend Architect");
+
     const architectPath = join(h.sourceRoot, "engineering", "engineering-backend-architect.md");
     rmSync(architectPath);
     expect(sync()).toMatchObject({ retired: 1 });
+    expect(prompt("run_retired")).not.toContain("# Skill: Backend Architect");
+    expect(prompt("run_retired")).toContain("# Skill: humanizer");
+    expect(prompt("run_before")).not.toContain("# Skill: Backend Architect");
+
     writeFileSync(architectPath, ARCHITECT_MD, "utf8");
     expect(sync()).toMatchObject({ imported: 0, restored: 1, upgraded: 0, retired: 0, failures: [] });
+    expect(prompt("run_restored")).toContain("# Skill: Backend Architect");
     expect(h.connection.db.prepare("select status from skill_definitions where org_id = ? and slug = 'engineering-backend-architect'").get(h.orgId))
       .toEqual({ status: "active" });
     expect(sync()).toMatchObject({ restored: 0, skipped: 3 });
     h.connection.close();
   });
 
-  test("legacy catalogue entries retire so every install mirrors the bundle, while their bindings keep working", () => {
+  test("legacy catalogue entries retire so every install mirrors the bundle", () => {
     const h = harness();
     const staged = stageBuiltinSkillsLibrary(h.sourceRoot, h.libraryRoot);
     h.connection.transaction(() => importStagedSkills(h.skills, h.orgId, staged));