We recently tidied up the audio wall within myriad but now when we schedule in auto track it reports carts with no audio or missing and quite a lot of songs are mismatched.

Sounds like you moved carts using the audiowall not via Autotrack - which moves the carts but doesn't then update the database entry.  So if you have song A on say cart 5000 and in the database as cart 5000.  If you then move that song in the audiowall, the song moves but the Autotrack entry still points to cart 5000.  If song B then gets put onto cart 5000, Autotrack still thinks it's Song A.  You have to move songs from within Autotrack.

As to the best way of sorting it out, I'm not sure.  If you've only done a few changes, you could try retracing all the movements and moving it all back again.

Neil