Dev tool Debugger breakpoints persist on a ghost file when refactor a folder

### Is there an existing issue for this?

- [X] I have searched the [existing issues](https://github.com/flutter/flutter/issues)
- [X] I have read the [guide to filing a bug](https://flutter.dev/docs/resources/bug-reports)

### Steps to reproduce

1. Have a breakpoint, for example: lib/screens/address/address.dart and i place a breakpoint at line 10
2. run the app as debug and open dev tool on browser then go to debugger and look at list of breakpoint
3. refactor, rename or delete route to that file any level

### Expected results

Breakpoint disappear or delete appropriately

### Actual results

Debugger will still display that file and breakpoint line, persist until i recreate folders and and that file to unmark a breakpoint

### Code sample

Code sample

```dart
//It a dev tool bug, i recreate the bug in the repo i linked with comment
```
https://github.com/TheValkDokk/bug

### Screenshots or Video

Screenshots / Video demonstration

[Upload media here]

### Logs

Logs

```console
[Paste your logs here]
```

### Flutter Doctor output

Doctor output

```console
[√] Flutter (Channel stable, 3.7.0, on Microsoft Windows [Version 10.0.22621.963], locale en-US)
• Flutter version 3.7.0 on channel stable at C:\Code\SDKs\Flutter\flutter_windows_3.3.10-stable\flutter
• Upstream repository https://github.com/flutter/flutter.git
• Framework revision b06b8b2710 (3 months ago), 2023-01-23 16:55:55 -0800
• Engine revision b24591ed32
• Dart version 2.19.0
• DevTools version 2.20.1

[√] Windows Version (Installed version of Windows is version 10 or higher)

[√] Android toolchain - develop for Android devices (Android SDK version 33.0.1)
• Android SDK at C:\Users\ValkDokk\AppData\Local\Android\sdk
• Platform android-33, build-tools 33.0.1
• Java binary at: C:\Program Files\Android\Android Studio\jre\bin\java
• Java version OpenJDK Runtime Environment (build 11.0.13+0-b1751.21-8125866)
• All Android licenses accepted.

[√] Chrome - develop for the web
• Chrome at C:\Program Files\Google\Chrome\Application\chrome.exe

[√] Visual Studio - develop for Windows (Visual Studio Community 2022 17.4.4)
• Visual Studio at C:\Program Files\Microsoft Visual Studio\2022\Community
• Visual Studio Community 2022 version 17.4.33213.308
• Windows 10 SDK version 10.0.22621.0

[√] Android Studio (version 2021.3)
• Android Studio at C:\Program Files\Android\Android Studio
• Flutter plugin can be installed from:
https://plugins.jetbrains.com/plugin/9212-flutter
• Dart plugin can be installed from:
https://plugins.jetbrains.com/plugin/6351-dart
• Java version OpenJDK Runtime Environment (build 11.0.13+0-b1751.21-8125866)

[√] VS Code (version 1.77.3)
• VS Code at C:\Users\ValkDokk\AppData\Local\Programs\Microsoft VS Code
• Flutter extension version 3.62.0

[√] Connected device (5 available)
• SM A715F (mobile) • R58N91GYWRB • android-arm64 • Android 13 (API 33)
• SM G988N (mobile) • 127.0.0.1:61187 • android-x64 • Android 7.1.2 (API 25)
• Windows (desktop) • windows • windows-x64 • Microsoft Windows [Version 10.0.22621.963]
• Chrome (web) • chrome • web-javascript • Google Chrome 112.0.5615.86
• Edge (web) • edge • web-javascript • Microsoft Edge 111.0.1661.54

[√] HTTP Host Availability
• All required HTTP hosts are available

• No issues found!
```