As the person that develops Budgie and also was the one that did the changes for Budgie that were deployed today, not only did none of my changes relate to anything regarding user files, but Budgie just doesn't do anything except modify its own settings (which ends up touching a single dconf file in your home directory), read gsettings and application desktop files, etc.
Sounds like user error to some degree or some other issue? But you're missing details, logs, etc.
