diff --git a/sdk/typescript/_bundled_plugin/scripts/workbench_native_indexes.py b/sdk/typescript/_bundled_plugin/scripts/workbench_native_indexes.py
index 8ce2492bc..39f844383 100644
--- a/sdk/typescript/_bundled_plugin/scripts/workbench_native_indexes.py
+++ b/sdk/typescript/_bundled_plugin/scripts/workbench_native_indexes.py
@@ -202,23 +202,29 @@ def list_repositories(
     for row in connection.execute(
         "SELECT id, target_id FROM scans ORDER BY started_at DESC, id DESC"
     ):
-        latest_scan_by_target.setdefault(row["target_id"], scans_by_id[row["id"]])
+        scan = scans_by_id.get(row["id"])
+        if scan is not None:
+            latest_scan_by_target.setdefault(row["target_id"], scan)
 
     open_findings_by_target = Counter(
         row["target_id"] for row in _indexed_findings(connection) if row["status"] == "open"
     )
     targets = {row["id"]: row for row in connection.execute("SELECT * FROM security_targets")}
+    target_ids = [
+        *latest_scan_by_target,
+        *(target_id for target_id in targets if target_id not in latest_scan_by_target),
+    ]
     repositories = [
         {
             "checkoutAvailable": Path(target["current_path"]).is_dir(),
             "displayName": target["display_name"],
-            "latestScan": latest_scan,
+            "latestScan": latest_scan_by_target.get(target_id),
             "openFindingsCount": open_findings_by_target.get(target_id, 0),
-            "scanCount": scan_count_by_target[target_id],
+            "scanCount": scan_count_by_target.get(target_id, 0),
             "targetId": target_id,
             "targetPath": target["current_path"],
         }
-        for target_id, latest_scan in latest_scan_by_target.items()
+        for target_id in target_ids
         if (target := targets.get(target_id)) is not None
     ]
     if args is None:
@@ -229,7 +235,8 @@ def list_repositories(
         repository
         for repository in repositories
         if (args.target_id is None or repository["targetId"] == args.target_id)
-        and args.status != "not_scanned"
+        and (args.status != "scanned" or repository["scanCount"] > 0)
+        and (args.status != "not_scanned" or repository["scanCount"] == 0)
         and (args.status != "open_findings" or repository["openFindingsCount"] > 0)
         and (
             not query
diff --git a/sdk/typescript/tests-ts/native-repository-index.test.ts b/sdk/typescript/tests-ts/native-repository-index.test.ts
new file mode 100644
index 000000000..05cb7f31a
--- /dev/null
+++ b/sdk/typescript/tests-ts/native-repository-index.test.ts
@@ -0,0 +1,108 @@
+import { spawnSync } from "node:child_process";
+import { join } from "node:path";
+import { expect, test } from "bun:test";
+import { PLUGIN_ROOT } from "./plugin-root.js";
+
+test("repository index includes and filters persisted unscanned targets", () => {
+  const python = Bun.which("python3") ?? Bun.which("python") ?? Bun.which("py");
+  expect(python).not.toBeNull();
+  const scripts = join(PLUGIN_ROOT, "scripts");
+  const probe = `
+import argparse
+import json
+import sqlite3
+import sys
+sys.path.insert(0, sys.argv[1])
+import workbench_native_indexes as indexes
+
+connection = sqlite3.connect(":memory:")
+connection.row_factory = sqlite3.Row
+connection.executescript("""
+CREATE TABLE security_targets (
+  id TEXT PRIMARY KEY,
+  current_path TEXT NOT NULL,
+  display_name TEXT NOT NULL
+);
+CREATE TABLE scans (
+  id TEXT PRIMARY KEY,
+  target_id TEXT NOT NULL,
+  started_at TEXT NOT NULL
+);
+""")
+connection.executemany(
+    "INSERT INTO security_targets VALUES (?, ?, ?)",
+    [
+        ("target-scanned", "/repo/scanned", "Scanned"),
+        ("target-unscanned", "/repo/unscanned", "Unscanned"),
+    ],
+)
+connection.execute(
+    "INSERT INTO scans VALUES (?, ?, ?)",
+    ("scan-1", "target-scanned", "2026-08-18T00:00:00Z"),
+)
+connection.commit()
+
+indexes.scan_history.list_scans = lambda _connection: {
+    "scans": [{"scanId": "scan-1", "targetId": "target-scanned"}]
+}
+indexes._indexed_findings = lambda _connection: iter(())
+
+def arguments(status):
+    return argparse.Namespace(
+        query=None,
+        target_id=None,
+        status=status,
+        offset=0,
+        limit=None,
+    )
+
+def compact(result):
+    return [
+        {
+            "targetId": row["targetId"],
+            "scanCount": row["scanCount"],
+            "latestScan": row["latestScan"],
+        }
+        for row in result["repositories"]
+    ]
+
+print(json.dumps({
+    "all": compact(indexes.list_repositories(connection)),
+    "scanned": compact(indexes.list_repositories(connection, arguments("scanned"))),
+    "notScanned": compact(indexes.list_repositories(connection, arguments("not_scanned"))),
+}))
+`;
+
+  const result = spawnSync(python!, ["-I", "-B", "-c", probe, scripts], {
+    encoding: "utf8",
+  });
+  expect(result.status, result.stderr).toBe(0);
+  expect(JSON.parse(result.stdout)).toEqual({
+    all: [
+      {
+        targetId: "target-scanned",
+        scanCount: 1,
+        latestScan: { scanId: "scan-1", targetId: "target-scanned" },
+      },
+      {
+        targetId: "target-unscanned",
+        scanCount: 0,
+        latestScan: null,
+      },
+    ],
+    scanned: [
+      {
+        targetId: "target-scanned",
+        scanCount: 1,
+        latestScan: { scanId: "scan-1", targetId: "target-scanned" },
+      },
+    ],
+    notScanned: [
+      {
+        targetId: "target-unscanned",
+        scanCount: 0,
+        latestScan: null,
+      },
+    ],
+  });
+});