I think this has been reported before, and presuming you are really using the correct styles, I believe the solution was to export each of the component docs to .idml, resave those as new .indd files, and rebuild the book with the new files. This will be a big problem if you've used inter-doc cross-references or hyperlinks.
I dont think Ive used inter-doc cross references, but I still have to do an index,
will it effect that?
should I do the index first?
also side question: I need to do a very thorough index, do you have any links that has good advice / instructions?
I don't think it will affect the index, but I'd wait until after, if possible, for safety.
I'm afraid I don't have any references for you on Indexing. Sorry.
It's good that you're looking into this before getting started.
Search Google for terms like "indexing books" without quotes.