Hello,
Maybe there's a setting that's got screwed....but I can't see which one would do that.
Have you changed the editor theme?
Editor settings are saved (on my computer at least) in C:\Users\username\AppData\Roaming\Godot\editor_settings-3.tres
You can rename that file and launch Godot and see if the files come back. A new .tres
file will be created, so you can quit Godot, delete that and rename the old file back to get your original settings.
If I turn on "show hidden files" in the editor, this is the line that gets saved in the file settings file:
filesystem/file_dialog/show_hidden_files = true
The edit settings file can be edited using a text editor.
Maybe upload your file and I'll try it on mine to see if I get the same thing.