Problems with iTunes Organizing Library

[Russell Bell]

I've been letting iTunes organize my music for years without problems, however lately, it seems iTunes is wrecking my library organization. Some tracks are duplicates, others are missing. Thankfully it is not widespread, and 95%+ of my library is still in good shape - however it is a pain to have some of my library corrupted. The problem is not just in iTunes, but in the folder organization as well (see attached image where about 10 tracks from a Band of Horses album have gone missing, and some tracks are now folders containing tracks from two Red Hot Chili Peppers albums and a Sublime album). Background info:

• I don't use iTunes Match or Apple Music
• I keep my music on a NAS and whenever iTunes gets "disconnected", I need to change my iTunes media folder location and say yes to "move and rename files in new iTunes folder location"
• All of my tracks are well tagged - this is confirmed by the fact that I have a Sonos which indexes my library based on tags (not folder structure) and all of my music is fine there

I don't have many playlists and I'm not too attached to my play counts (I've had my library go bad too many times before and now just rely on last.fm). Is my best move to delete everything from iTunes, keep the original files, then move all of my music back into the "Automatically Add to iTunes" folder and let it reimport itself right?

Also, how can I prevent this from happening again?