This question already has an answer here:
I have a large Acrobat file (currently 92 pages, 25MB) which is constructed from lots of different sources (1 InDesign and 80 Illustrator files). Since I first brought these sources together, each page of it has been replaced a good dozen times, and the file is starting to creak under the weight. Acroat is giving me warnings about possible corruption, and crashes occasionally when saving.
No data has been lost yet, but it's enough to give me pause. I could reconstruct the file from sources if I had to, but it would take forever to get all the bookmarks and links set up just the way they used to be.
Is there any way of getting Acrobat to rebuild the file from the ingredients and make it easier to work with?