diff --git a/src/lib/bun-runtime-preflight.ts b/src/lib/bun-runtime-preflight.ts
index 19b9ca3ca09..3f3e7f6a68b 100644
--- a/src/lib/bun-runtime-preflight.ts
+++ b/src/lib/bun-runtime-preflight.ts
@@ -19,9 +19,10 @@ export class RuntimePreflightError extends Error {
   }
 }
 
-type DirectoryIdentity = { dev: number; ino: number; isDirectory(): boolean; isSymbolicLink(): boolean };
+// bigint: NTFS file IDs exceed 2^53, where adjacent IDs are equal as numbers.
+type DirectoryIdentity = { dev: bigint; ino: bigint; isDirectory(): boolean; isSymbolicLink(): boolean };
 export interface RuntimePreflightFs {
-  lstatSync: (path: string) => DirectoryIdentity;
+  lstatSync: (path: string, options: { bigint: true }) => DirectoryIdentity;
   mkdirSync: (path: string, mode: number) => unknown;
   rmdirSync: (path: string) => void;
   readdirSync: (path: string) => readonly string[];
@@ -44,7 +45,7 @@ export interface RuntimePreflightDeps {
 const probeFs: RuntimePreflightFs = { lstatSync, mkdirSync, rmdirSync, readdirSync };
 
 function sameDirectory(fs: RuntimePreflightFs, path: string, owned: DirectoryIdentity): boolean {
-  const current = fs.lstatSync(path);
+  const current = fs.lstatSync(path, { bigint: true });
   return current.isDirectory() && !current.isSymbolicLink()
     && current.dev === owned.dev && current.ino === owned.ino;
 }
@@ -59,7 +60,7 @@ function removeOwnedEmptyDirectory(fs: RuntimePreflightFs, path: string, owned:
 function prepareRoot(fs: RuntimePreflightFs, root: string, rootWasAbsent?: boolean): void {
   try {
     if (rootWasAbsent === undefined) {
-      try { fs.lstatSync(root); rootWasAbsent = false; }
+      try { fs.lstatSync(root, { bigint: true }); rootWasAbsent = false; }
       catch (error) {
         if ((error as NodeJS.ErrnoException).code !== "ENOENT") throw error;
         rootWasAbsent = true;
@@ -73,7 +74,7 @@ function prepareRoot(fs: RuntimePreflightFs, root: string, rootWasAbsent?: boole
         // Use a concurrently created root, subject to the directory check below.
       }
     }
-    const current = fs.lstatSync(root);
+    const current = fs.lstatSync(root, { bigint: true });
     if (!current.isDirectory() || current.isSymbolicLink()) throw new RuntimePreflightError("create");
   } catch {
     throw new RuntimePreflightError("create");
@@ -83,7 +84,7 @@ function prepareRoot(fs: RuntimePreflightFs, root: string, rootWasAbsent?: boole
 function probeInProcess(fs: RuntimePreflightFs, path: string): void {
   let owned: DirectoryIdentity | undefined;
   try {
-    try { fs.mkdirSync(path, 0o700); owned = fs.lstatSync(path); }
+    try { fs.mkdirSync(path, 0o700); owned = fs.lstatSync(path, { bigint: true }); }
     catch { throw new RuntimePreflightError("create"); }
     try { fs.rmdirSync(path); }
     catch { throw new RuntimePreflightError("remove"); }
@@ -96,10 +97,10 @@ function probeChild(runtime: DurableBunRuntime, path: string, nonce: string, spa
   // The child emits only this invocation's nonce and a fixed result, never paths/errors.
   const script = `const fs = require("node:fs"); const path = ${JSON.stringify(path)};
 let result = "create", owned;
-try { fs.mkdirSync(path, 0o700); owned = fs.lstatSync(path); result = "remove";
+try { fs.mkdirSync(path, 0o700); owned = fs.lstatSync(path, { bigint: true }); result = "remove";
   fs.rmdirSync(path); result = "ok";
 } catch { /* result already names the failed step; details never leave the child */ } finally {
-  if (owned) { try { const now = fs.lstatSync(path);
+  if (owned) { try { const now = fs.lstatSync(path, { bigint: true });
     if (now.isDirectory() && !now.isSymbolicLink() && now.dev === owned.dev && now.ino === owned.ino
       && fs.readdirSync(path).length === 0) fs.rmdirSync(path);
   } catch { /* leave any probe entry that cannot be proven ours */ } }
diff --git a/tests/lib/bun-runtime-preflight.test.ts b/tests/lib/bun-runtime-preflight.test.ts
index 353302af64d..0c7dea985ff 100644
--- a/tests/lib/bun-runtime-preflight.test.ts
+++ b/tests/lib/bun-runtime-preflight.test.ts
@@ -171,18 +171,44 @@ describe("selected Bun write preflight", () => {
   test("a replacement empty root with a different inode survives refusal", () => {
     const parent = temporary();
     const root = join(parent, "replaced");
-    let originalIno = 0;
+    let originalIno = 0n;
     refusal(() => assertSelectedRuntimeWritable(runtime, root, {
       ...windows, rootWasAbsent: true, spawnSync: (() => {
-        originalIno = lstatSync(root).ino;
+        originalIno = lstatSync(root, { bigint: true }).ino;
         renameSync(root, join(parent, "old")); mkdirSync(root);
         return { status: 1, stdout: "nonce:create" };
       }) as typeof spawnSync,
     }), "create");
-    expect(lstatSync(root).ino).not.toBe(originalIno);
+    // NTFS file IDs exceed 2^53; as numbers, adjacent IDs compare equal.
+    expect(lstatSync(root, { bigint: true }).ino).not.toBe(originalIno);
     expect(readdirSync(root)).toEqual([]);
   });
 
+  test("a replacement probe whose file ID differs only above 2^53 is never removed", () => {
+    const root = temporary();
+    const probe = join(root, ".ocx-runtime-probe-nonce");
+    let replaced = false;
+    let removals = 0;
+    // Adjacent IDs above 2^53 collapse to one Number: the owned probe and its replacement.
+    const lstat = ((path: string, options?: { bigint?: boolean }) => {
+      const real = lstatSync(path, { bigint: true });
+      const ino = path === probe ? (replaced ? 2n ** 53n : 2n ** 53n + 1n) : real.ino;
+      return {
+        dev: options?.bigint ? real.dev : Number(real.dev), ino: options?.bigint ? ino : Number(ino),
+        isDirectory: () => real.isDirectory(), isSymbolicLink: () => real.isSymbolicLink(),
+      };
+    }) as RuntimePreflightFs["lstatSync"];
+    refusal(() => assertSelectedRuntimeWritable(standalone, root, {
+      ...windows, fs: { ...fs, lstatSync: lstat, rmdirSync: path => {
+        if (removals++ > 0) { rmdirSync(path); return; }
+        renameSync(path, join(root, "owned-probe")); mkdirSync(path); replaced = true;
+        throw new Error("denied once");
+      } },
+    }), "remove");
+    expect(existsSync(probe)).toBe(true);
+    expect(removals).toBe(1);
+  });
+
   test("refusal never inspects emptiness or deletes the config root", () => {
     const root = join(temporary(), "root");
     const cleanup: string[] = [];
diff --git a/tests/providers/cc-switch-import.test.ts b/tests/providers/cc-switch-import.test.ts
index 185f1a7ab85..106475de1bd 100644
--- a/tests/providers/cc-switch-import.test.ts
+++ b/tests/providers/cc-switch-import.test.ts
@@ -1006,7 +1006,10 @@ describe("CC-Switch keyless provider import", () => {
     try {
       writer.run("PRAGMA journal_mode = WAL;");
       writer.run("CREATE TABLE providers (id TEXT NOT NULL, app_type TEXT NOT NULL, name TEXT NOT NULL, settings_config TEXT NOT NULL, sort_index INTEGER, PRIMARY KEY (id, app_type))");
-      writer.prepare("INSERT INTO providers VALUES (?1, ?2, ?3, ?4, ?5)").run(
+      // writer.run finalizes its statement; an unfinalized prepare() keeps the db, -wal and -shm
+      // open past close(), and Windows then refuses to delete the temp tree (EBUSY).
+      writer.run(
+        "INSERT INTO providers VALUES (?1, ?2, ?3, ?4, ?5)",
         "existing-prov",
         "openai",
         "Existing",
@@ -1017,10 +1020,12 @@ describe("CC-Switch keyless provider import", () => {
 
       // Disable auto-checkpoint so subsequent UPDATE and INSERT stay exclusively in live-wal.db-wal.
       writer.run("PRAGMA wal_autocheckpoint = 0;");
-      writer.prepare("UPDATE providers SET settings_config = ?1 WHERE id = 'existing-prov'").run(
+      writer.run(
+        "UPDATE providers SET settings_config = ?1 WHERE id = 'existing-prov'",
         JSON.stringify({ baseUrl: "https://updated.acme.example/v1" }),
       );
-      writer.prepare("INSERT INTO providers VALUES (?1, ?2, ?3, ?4, ?5)").run(
+      writer.run(
+        "INSERT INTO providers VALUES (?1, ?2, ?3, ?4, ?5)",
         "uncheckpointed-prov",
         "claude",
         "Uncheckpointed",