Comentário oficial
This happened because you allowed iTunes to manage the files. When you change the metadata, (like the album / artist / song name) it automatically changes the filename or path. This isn't a problem within iTunes itself, but as soon as you link to external programs which have built a database and point to a specific file at a specific path, when you make those changes, you break the link.
You have two choices...
1) Wipe out the rekordbox database and spend hours re-creating the cue points.
2) Spend hours relocating the songs one-by-one.
I would recommend the latter, it may be pretty quick using the search. But I would also recommend you disable the iTunes music management feature (in the preferences), and then use the Sync Manager in rekordbox to bring your music from iTunes in future.