diff --git a/packages/codegraph/entrypoint.sh b/packages/codegraph/entrypoint.sh
index 24fc35d..cc44711 100644
--- a/packages/codegraph/entrypoint.sh
+++ b/packages/codegraph/entrypoint.sh
@@ -39,13 +39,19 @@ run_import() {
   fi
 
   # Run import (additive — never prunes on boot; use `import-skills --full` manually for that)
-  node dist/cli.js import-skills "$DATA_DIR" 2>&1
+  BEFORE=$(sqlite3 "$DATA_DIR/.codegraph/graph.db" "SELECT COUNT(*) FROM skills;" 2>/dev/null || echo "?")
+  if node dist/cli.js import-skills "$DATA_DIR" 2>&1; then
+    AFTER=$(sqlite3 "$DATA_DIR/.codegraph/graph.db" "SELECT COUNT(*) FROM skills;" 2>/dev/null || echo "?")
+    echo "Skill catalog: ${BEFORE} -> ${AFTER} skills"
+    # Record the imported bundle hash ONLY on success, so a failed import retries
+    # on the next boot instead of being permanently masked by a stale hash.
+    [ -n "$BUNDLE_HASH" ] && printf '%s' "$BUNDLE_HASH" > "$HASH_FILE"
+  else
+    echo "WARNING: skill import FAILED (exit $?) — catalog.hash left unchanged so the next boot retries." >&2
+  fi
 
   # Cleanup symlinks (data stays in SQLite)
   rm -rf "$DATA_DIR/.opencode" "$DATA_DIR/.agents"
-
-  # Record the imported bundle hash so unchanged redeploys skip the import.
-  [ -n "$BUNDLE_HASH" ] && printf '%s' "$BUNDLE_HASH" > "$HASH_FILE"
 }
 
 if [ "$SKILL_COUNT" = "0" ] || [ "$SKILL_COUNT" = "" ]; then
diff --git a/packages/storage/src/import-skills.ts b/packages/storage/src/import-skills.ts
index 2af68ba..d35a64c 100644
--- a/packages/storage/src/import-skills.ts
+++ b/packages/storage/src/import-skills.ts
@@ -368,7 +368,13 @@ export function importSkills(
 
   // Optional full-sync: deprecate active skills that vanished from the bundle.
   let pruned = 0
-  if (opts.prune) {
+  if (opts.prune && skills.length === 0) {
+    // Safety guard: an empty discovered set almost always means the bundle path
+    // was wrong (e.g. `import-skills /data` without the .opencode/.agents symlinks
+    // that entrypoint.sh sets up), NOT an intent to deprecate the entire catalog.
+    // Refuse to prune — otherwise a misconfigured path silently wipes every skill.
+    console.warn('[import-skills] --full: 0 skills discovered — skipping prune to avoid deprecating the whole catalog. Check the workspace path.')
+  } else if (opts.prune) {
     const discovered = new Set(skills.map((s) => s.name))
     const activeNames = (db
       .prepare(`SELECT name FROM skills WHERE status = 'active' AND category NOT IN ('System','Lifecycle')`)
diff --git a/packages/storage/tests/import-skills.test.ts b/packages/storage/tests/import-skills.test.ts
index 441f772..a490bd3 100644
--- a/packages/storage/tests/import-skills.test.ts
+++ b/packages/storage/tests/import-skills.test.ts
@@ -109,4 +109,29 @@ describe('importSkills()', () => {
       db.close()
     }
   })
+
+  it('--full does NOT prune when the bundle is empty (0 skills discovered)', () => {
+    const workspace = makeWorkspace() // no .claude/skill — nothing to discover
+    importSkills(workspace)           // creates the DB, imports 0 skills
+
+    // Seed an active catalog skill directly (simulates an existing prod catalog).
+    const dbPath = path.join(workspace, '.codegraph', 'graph.db')
+    const seed = new Database(dbPath)
+    seed.prepare(
+      `INSERT INTO skills (name, category, description, content, type, tags, lines, updated_at, status)
+       VALUES ('keepme', 'Backend', 'd', '#', 'domain', '[]', 1, ?, 'active')`,
+    ).run(new Date().toISOString())
+    seed.close()
+
+    // --full against an empty bundle must NOT deprecate the existing catalog.
+    const result = importSkills(workspace, { prune: true })
+    expect(result.pruned).toBe(0)
+
+    const db = new Database(dbPath)
+    try {
+      expect((db.prepare("SELECT status AS s FROM skills WHERE name = 'keepme'").get() as { s: string }).s).toBe('active')
+    } finally {
+      db.close()
+    }
+  })
 })