diff --git a/server/src/__tests__/company-skills-routes.test.ts b/server/src/__tests__/company-skills-routes.test.ts
index f5e7feb3..fdc74a54 100644
--- a/server/src/__tests__/company-skills-routes.test.ts
+++ b/server/src/__tests__/company-skills-routes.test.ts
@@ -278,31 +278,24 @@ describe("company skill mutation permissions", () => {
     expect(mockCompanySkillService.scanProjectWorkspaces).toHaveBeenCalledWith("company-1", {});
   });
 
-  it("returns skipped and conflicts from scan including pruned skill conflicts", async () => {
+  it("returns warnings from scan when removed skills are still used by agents", async () => {
     mockAgentService.getById.mockResolvedValue({
       id: "agent-1",
       companyId: "company-1",
       permissions: { canCreateAgents: true },
     });
 
-    const skippedSkill = { id: "skill-1", slug: "removed-skill", name: "Removed Skill" };
-    const conflictEntry = {
-      path: "https://github.com/vercel-labs/agent-browser",
-      existingSkillId: "skill-2",
-      existingSkillKey: "vercel-labs/agent-browser/ghost-skill",
-      existingSourceLocator: "https://github.com/vercel-labs/agent-browser",
-      reason: 'Skill "ghost-skill" was removed from https://github.com/vercel-labs/agent-browser but is still used by Builder. Detach it from those agents first.',
-    };
-
     mockCompanySkillService.scanProjectWorkspaces.mockResolvedValueOnce({
       scannedProjects: 1,
       scannedWorkspaces: 1,
       discovered: [],
       imported: [],
       updated: [],
-      skipped: [skippedSkill],
-      conflicts: [conflictEntry],
-      warnings: [],
+      skipped: [],
+      conflicts: [],
+      warnings: [
+        'Skill "ghost-skill" was removed from https://github.com/vercel-labs/agent-browser but is still used by Builder. It will not be automatically removed.',
+      ],
     });
 
     const res = await request(await createApp({
@@ -316,12 +309,7 @@ describe("company skill mutation permissions", () => {
 
     expect(res.status, JSON.stringify(res.body)).toBe(200);
     expect(res.body).toMatchObject({
-      skipped: [{ id: "skill-1", slug: "removed-skill" }],
-      conflicts: [{
-        path: "https://github.com/vercel-labs/agent-browser",
-        existingSkillId: "skill-2",
-        reason: expect.stringContaining("was removed from"),
-      }],
+      warnings: [expect.stringContaining("was removed from")],
     });
   });
 
diff --git a/server/src/services/company-skills.ts b/server/src/services/company-skills.ts
index 397db7af..a95b9ebb 100644
--- a/server/src/services/company-skills.ts
+++ b/server/src/services/company-skills.ts
@@ -2044,16 +2044,11 @@ export function companySkillService(db: Db) {
           if (currentSlugs.has(skill.slug)) continue;
           const usedByAgents = await usage(companyId, skill.key);
           if (usedByAgents.length > 0) {
-            conflicts.push({
-              path: sourceLocator,
-              existingSkillId: skill.id,
-              existingSkillKey: skill.key,
-              existingSourceLocator: sourceLocator,
-              reason: `Skill "${skill.slug}" was removed from ${sourceLocator} but is still used by ${usedByAgents.map((a) => a.name).join(", ")}. Detach it from those agents first.`,
-            });
+            warnings.push(
+              `Skill "${skill.slug}" was removed from ${sourceLocator} but is still used by ${usedByAgents.map((a) => a.name).join(", ")}. It will not be automatically removed.`,
+            );
           } else {
-            const deleted = await deleteSkill(companyId, skill.id);
-            if (deleted) skipped.push(deleted);
+            await deleteSkill(companyId, skill.id);
           }
         }
       } catch {