Give this a try http://forums.adobe.com/thread/526991
Also, are you using any font management systems, what fonts are reported missing that you can't change, any other info?
Have you tried creating an new document with identical Document Setup, margins and bleeds, and then use the Pages Panel sub menu to "Move Pages" and select the new document as the destination.
When you do this can you change the font?
I tried to export it as an IDML and it crashes. This isn't my computer so I'm not sure about the font management system, I'm learning InDesign on the fly so to speak.
The 'missing' fonts are: Clarendon BT Heavy and Minion Pro Heavy. They should be Minion Pro Regular, which is what our designer changed it to before she left (I fibbed a bit in the original question to simplify the matter, but now I see it's much more complex then I thought).
So I tried to trash the preferences, but nothing happened, although with that particular exercise I'm not 100% sure I'm doing it right. As it's not my computer I don't feel right just deleting the files, so I moved them and nothing happened.
Also now when I try to change the fonts (with or without the old preferences), all of the type around it changes to Batang Regular and I can't change it back. I have no idea why, possibly this is also what the typesetter originally used?
The whole document is 200 pages long, so I'm a bit loath to restart the whole process, but it might have to happen... that said if the font is the problem, copying the text would only make it carry across right?
Thanks for the advise!