Rekordbox reads the tracks from where they are stored, so it thinks and sees ITunes as the pathway.  Once you change it it won't find the file.  You'll have to move your library to another spot and then repopulate your playlists by finding the tracks and then placing them in the playlists. 

Rekordbox only sees the data and plays tracks, like Serato and other sw it needs to find what you have stored on your machine.

Thanks for your reply.

How would be best to this?

@stephen > I think the problem might be more that you have iTunes set to manage the location of your audio files; if that's the case, if you delete them from iTunes, you're not just deleting the entry in the iTunes library (database), you're physically deleting the file from your computer, hence rekordbox is unable to locate the file once you've removed it from iTunes.

My recommendation is to first check that setting within iTunes (go to Preferences > Advanced and see if the "Keep iTunes Media folder organized" box is ticked), if it is, you'll want to move all your music out of the iTunes folder and stick it in your Music folder (location varies between Mac and PC, but not hard to find them / move it).

Let us know if you need more detail on that last step.