The October 2018 Update tried to tidy up this situation. When KFR is being used, the October 2018 Update will delete the original, default Known Folder locations. Microsoft imagined that this would simply remove some empty, redundant directories from your user profile. No need to have a Documents directory in your profile if you’re using a redirected location, after all. The problem is, it neither checked to see if those directories were empty first, nor copied any files to the new redirected location. It just wiped out the old directory, along with anything stored within it. Hence the data loss.

Maybe just leave tidying to the user.