Just found this thread and think I have a related question... hopefully tt2 is still around.
Backstory - accidentally unplugged external HD on which iTunes library and media is stored a couple of days ago. iTunes freaked out a little later saying it couldn't find the library file etc, though it the external was plugged back in and looked ok.
So my previous iTunes library/media organization was perfect - everything in /Music/iTunes/iTunes Media. In the process of trying to fix the external issue, I noticed my preferences > advanced > iTunes media folder location was blank so I erroneously changed the folder one level up, to /Music/iTunes, with the keep organized clicked and probably said yes to some consolidation popup. Anyway, long story short, MOST of my media has moved itself up to /Music/iTunes, though strangely a few items remain under /Music/iTunes/iTunes Media, and now I want it all back under iTunes Media and not at the upper level. I've tried a lot of the tips in this thread, what with the uncheck and check the Keep Organized etc, but nothing will move back under the old iTunes Media structure.
Can you help?