FWIW, I just wanted to add that I keep my list clean by making a MAP file and then copying only the roms in my MAP file to a seperate directory using the Map File Maker app. There's a feature to load a MAP file, set an input and output directory, and move these roms. I know it's not the solution you're hoping for but my list is neat and clean. Obviously this will not fix your database issue or filter non-working roms or anything, but I added that so I can keep only games I personally want on the server and 7-zip the full set for archiving. Hope that helps!