investigate cache invalidation of preloaded scripts with CACHE_MODE_REPLACE_DEEP since 4.3

@ZackeryRSmith found out scripts from preloaded scenes can be modded when loading with the new CACHE_MODE_REPLACE_DEEP added to 4.3 in [godotengine#88664](https://github.com/godotengine/godot/pull/88664)

```gdscript
ResourceLoader.load("scene path here", "", ResourceLoader.CACHE_MODE_REPLACE_DEEP)
```

ref [discord message](https://discord.com/channels/1028191864966361178/1128602076990152775/1382092867836580110)

we'll have to check if we can

- [x] do this with every preloaded scene to refresh scripts (`preload("...tscn")` containing a script)
- [ ] do this with directly preloaded scripts `preload("...gd")`
- [ ] if not, if we can add a script to a scene as subresource and then load it to refresh the script too