Thanks for your reply, Paul, and sorry for posting twice. I didn’t realize you’re probably moderating posts before they show up in the forum.
Anyway, here’s what I did now. I moved a backup version of my library to iTunes and deleted the rubbish version that resulted from SongKong. I then pointed iTunes to the new (i.e. original) library and everything was back to normal.
Now, I ran SongKong again following your advice with BOTH options under advanced tab in iTunes disabled (organize & manage). I also used the wizard in SongKong to prepare your app for iTunes. Double-checked that BOTH “Save to iTunes” and “Rename Files based on Metadata” (I use “Yes, if matched to release or song”) are activated. I then went to the naming tab and selected all the iTunes specific formats (as I thought this might cause a problem).
Thing is, after 4h of working on my library, that SongKong produced the same crap. Approximately 80% of songs are reported as missing. My guess is that the ones that work weren’t renamed because they didn’t match a release or song. The majority though seems to be lost by iTunes.
The question now is WHY? Because SongKong should notify iTunes of the changes and iTunes should act on them accordingly.