Godot overwrites custom editor theme

### Tested versions

4.6.stable

### System information

linux

### Issue description

I've been using my own custom editor theme for a while, and didn't touched theme settings since like some 4.5-ish version. Today I adjusted font size a bit and it totally nuked my custom theme that had a lot of overrides with bunch of standard spacing overrides! My bad not having a backup of course, but obviously this is destructive bug.
P.S.: I'm not sure what's actually caused this; I've also did some asset movement (not touching the theme ofc, but it was in project root dir) and seen a blink of "Reimporting assets" during that session of death but I doubt it borked the theme (too much coincedence with spacing options from the EditorSettings). Yes, I can't reproduce.

### Steps to reproduce

1. Create custom theme with bunch of overrides
2. Set it as custom editor theme in editor settings
3. Touch some options here and there, I did font size and scaling with editor reload but had some others set before (like modern theme and minimal spacing)
4. If not, maybe do some manipulations in FileSystem that triggers asset reimport
5. Hope you catch that bug borking your theme

### Minimal reproduction project (MRP)

Any

Start by reproducing the editor-settings changes described on Linux, including custom theme overrides, font size or scaling changes, and any asset reimport triggered from the FileSystem. Compare the saved custom theme before and after the editor reload; done means these settings no longer destroy the custom theme. No source files or tests are identified in the report.

Written by the indexing model from the issue text.