We have all the photos on one primary system and then copy them to others as a form of backup -- except it's been screwed up for months so that, every time I access it, it keeps sending me new copies of stuff I already have. It keeps them within their original folders, at least, so not nearly as annoying as your situation, but even what I'm dealing with is frustrating enough I'm not getting anything done on that front.
Props to you for tackling and making progress against a much bigger problem.