Originally Posted by iatheia
The problem was that even though all the chapters originally appeared in order, Sigil can't recognize it and arranges them almost randomly.
I'm aware that Sigil doesn't handle EpubMerge's output very well. But I think it's an issue with Sigil, not EpubMerge. It's on my wish list of things to do to look at Sigil's import code someday.
I'm not familiar with dotepub.com. I'll have to take a look at it. (EpubMerge does have a little bit of special code for making merges of FFDL epubs nicer than usual.)
If re-converting fixed your TOC issue, I wonder if using EpubMerge's Flatten TOC option would have helped.