Export to EPUB from INDB multiplies several common problems with hyperlinks. The first solution is not to use a Book structure, but put all source content in one INDD file. (The reasons for using Book structure are almost entirely related to print output anyway; EPUB export gains nothing from the separated files.
Beyond that, it's a matter of having meticulous component files in a fully updated and synchronized Book, and then checking and fixing each cross-chapter link one at a time without making ANY other edits or changes. Yep, it's a PITA.
If the files have been edited a lot (many sessions of edit-and-save), you can improve the odds by purging each INDD file (save to IDML, then open and save under a new name as INDD), then creating a new Book to hold them, and then testing and fixing the links. Files bloaded with undo info and other junk often fail to export correctly even when you can't find a specific problem.