That's never happened to me.
These are the file paths for Godot's settings:
https://docs.godotengine.org/en/stable/tutorials/io/data_paths.html#editor-data-paths
I suggest keeping those files backed up, and when Godot says you have no projects, compare the current files with the most recent backup, and see what the differences are.
On Linux, I use BackInTime, scheduled to run hourly, and include those files in the backups.