Godot version

4.2 rc1

System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

Issue description

When you preload() a script or a scene (or possibly anything else), that resource will stay in memory in its original form and it's difficult to remove or update it. This leads to all sorts of issues, particularly when the initial loading fails the resource will be broken until editor restart or in worst case until the user performs some magic to fix the cached version (when restarting doesn't work).

Here's the list of issues caused by this behavior:

• Moving or renaming scenes in the editor or changing properties in custom resources causes scene corruption #84981
• Godot fails to open a scene, claiming a script is missing, but the script is there! #79840
• Scene file became corrupted/invalid. #80324
• Built-in script of preloaded scene requires editor restart to become tool #81498
• Using other scripts by their class_name in an import plugin causes import to fail #81615
• Scene is invalid/corrupt according to the Godot editor, but works normally ingame #79545

These two issues are solved, but they were related, so adding for context:

• Opening a currently preloaded scene will remove paths from sub-resources #72854
• Crash when opening preloaded scene #80812

Related PRs (they don't fix the problem, but band-aid it partially):

• Fix behavior of ResourceFormatLoader CACHE_MODE_REPLACE (reverted) #84167 - helps reloading broken scenes
• Properly change global class paths on move or rename in the filesystem dock #85037 - prevents corruption issues when moving class files

Steps to reproduce

1. Use preload()
2. Pray it won't cause problems (it will 😉)

Minimal reproduction project

N/A