diff --git a/packages/cli/src/utils/backupPackageFile.ts b/packages/cli/src/utils/backupPackageFile.ts
index 9655ddf9..1fce781d 100644
--- a/packages/cli/src/utils/backupPackageFile.ts
+++ b/packages/cli/src/utils/backupPackageFile.ts
@@ -1,11 +1,35 @@
 import fs from 'node:fs';
 import path from 'node:path';
+import process from 'node:process';
+
+const windowsPathRegex = /^(?:[a-zA-Z]:|[\\/]{2}[^\\/]+[\\/]+[^\\/]+)?[\\/]$/;
+
+export const isRootPath = (path: string) => {
+  if (typeof path !== 'string') {
+    throw new TypeError('Expected a string');
+  }
+
+  path = path.trim();
+
+  // While it's unclear how long a root path can be on Windows, it definitely cannot be longer than 100 characters.
+  if (path === '' || path.length > 100) {
+    return false;
+  }
+
+  return process.platform === 'win32' ? windowsPathRegex.test(path) : path === '/';
+};
 
 export const backupFile = (runtimeSource: string, file: string) => {
+  if (isRootPath(runtimeSource)) {
+    return;
+  }
+
   const filePath = path.join(runtimeSource, file);
 
   if (fs.existsSync(filePath)) {
     fs.copyFileSync(filePath, `${filePath}.bak`);
+  } else {
+    backupFile(path.resolve(runtimeSource, '..'), file);
   }
 };
 
@@ -26,11 +50,17 @@ export const backupLock = (runtimeSource: string, npmType: string) => {
 };
 
 export const restoreFile = (runtimeSource: string, file: string) => {
+  if (isRootPath(runtimeSource)) {
+    return;
+  }
+
   const filePath = path.join(runtimeSource, file);
 
   if (fs.existsSync(filePath)) {
     fs.unlinkSync(filePath);
     fs.renameSync(`${filePath}.bak`, filePath);
+  } else {
+    restoreFile(path.resolve(runtimeSource, '..'), file);
   }
 };