Cross-references keep breaking for no apparent reason

I am currently working on a book with about 16 documents and literally thousands of cross-references.

Every time I open the documents, there are 5-12 broken cross-references in each document. I fix them all, and the next time I open the documents it might be the same ones broken again, or it might be different ones.

For example, there might be three specific pages that are "problematic," and many -- but not all -- cross-reference (across all the documents) pointing to those pages will be broken. I fix them all. Then the next day, maybe the same 3-4 pages or maybe a different 3-4 pages will be problematic, and many -- but not all -- cross-references pointing to THOSE pages will be broken. Nothing about the source pages has changed. 

Does anyone know why this might be happening? Or what I can do to prevent it from continuing to happen? 

The project is nearly done, so I'm considering just ignoring the broken cross-references for now, and then having that be my final step before exporting (so hopefully they don't have a chance to rebreak).