Thanks for the ideas gents. I managed to push the deadline back by finishing the other issues first (I work on 3 magazine issues at a time) and will redo this one from the beginning.
Thomaso, It was from 'add from file'. The file the that I took the pages from works fine, if this is what caused the issue. I'm now adding the shift key to that cmd-s to make sure I have several save files.
Firstdefence, thanks for that mate, I think that would have worked if I'd done it straight away. Unfortunately I was working on a few documents at the same time which would have overwritten the file. I' definitely remember that for next time.