Jaffa - can you copy files between other folders within internal memory? If so, I would...
1. copy all the music from the music folder into a folder called music1 and then delete the original music folder.
2. Reset your prime
3. See if the music folder has reappeared - if yes, try copying back into it. If not open the music player & play some music from music1 & then check to see if the music folder has been recreated. If it has, try copying into it again. If not, create it again yourself and try copying into it again.
The whole thing sounds suspiciously like the sort of bug commonplace to the new release of a new version of an os - ICS in this case.