How to Fix Duplicated Pages in InDesign When Exporting to Reflowable EPUB

Okay, I think two factors are in play here. First, I've never seen an EPUB export duplicate contents; if it's in the INDD, it goes into the EPUB, and if it shows up in the EPUB, it's in the work file somewhere. So those two pages are real artifacts somewhere in your file.

Second, junk that ends up at the end of an export is elements that were not anchored anywhere, so they are exported last, as secondary flow elements. (It's really common for novices to have their TOC end up at the end, because the TOC frame has to be anchored to text somewhere near the beginning to stay there.)

So I think you've accidentally duplicated those pages somehow, possibly by inadverently hitting Alt-arrow to copy+move a text frame. Two ways to check —

• Go to each of those pages and drag the text frame an inch or so out of position. Does a duplicate magically appear? Delete it.
• If not, the duplicate material may be hiding somewhere off the pages, out on the artboard. You can zoom out in Normal mode and page through, looking for junk frames out there in the wastelands. Or, maybe easier, search ("Document") for unique text on each page. Bet you find a hit somewhere odd. Again, delete that duplicated frame. (Note that if the frames are aligned, you'll get what appears to be a double hit on the same page; watch for that.)

And if not, there might not be any way to guess what's up without seeing your file. Report back with details of success or failure. 🙂