Okay. Endnotes are a problem about 75% of the time. Here's the quick test: Create a copy of the book file. Delete the End Notes text frame, contents and all. See if it exports. (It probably will.)
This means you have to fix your end note links. Re-do a few at a time (any reasonable subset of the total), save, and try the export. If you're lucky, you'll find and fix the bad one early on.
No, there's not really any better process. You can try doing an export as the absolute first operation after a reboot, ID open and file open, and that sometimes bypasses whatever gremlin causes this glitch. But not always.
—