Opening a currently preloaded scene will remove paths from sub-resources

[KoBeWi]

Godot version

4.0 a05670c

System information

Windows 10 x64

Issue description

Follow-up to #72257
The PR fixed only half of the issue. Sub-resource IDs are no longer lost, but paths still are. When a scene is preloaded in a currently opened script, opening that scene will result in all sub-resources having empty paths until you save it. While it's harmless in most cases, it's a major pain for built-in scripts, because they appear as [unsaved] in the script editor (which leads to further issues, like not being closed on scene close or not being able to open multiple scripts).

godot.windows.editor.dev.x86_64_XCY1o59Wgj.mp4

As identified in #72257 (comment), the issue is caused by preload() using resource cache in a wrong way. This needs a GDScript fix (and #72257 can be then reverted).

Steps to reproduce

1. Create a scene
2. Close it
3. Preload it in a script
4. Open again

Minimal reproduction project

PreloadBug.zip

[KoBeWi]

Further issues with affected built-in scripts include not being able to use breakpoints and not being able to pin-point errors (their source shows as something like GDScript:-143434353, which is the default Object string that displays id). Which means the issue also exists at runtime and is even worse.

[dalexeev]

• Possibly related: preload not works for custom ResourceFormatLoader #80131.