OK, awesome. I have a good idea of what files are actually missing now, so maybe I can prevent it from happening in the future:
1) I edited some artist names in MusicBee which caused path problems; is there a setting I can turn on so that those changes are applied to the folder itself? (if not retroactively, in the future?)
2) Is "automatically sweep and organize new files" the setting I want to turn on if I want everything I add to my library in the future to be copied to the same directory?