@kovidgoyal: I just uploaded a ticket with the debug log and copyrighted book files. It's flagged security because I wasn't sure how else to make it private.
@DNSB - The H1/H2 does match up to what I saw too. I think opening the ePub directly in ebook-edit and saving as ePub will also get something close.
This is part of my 'send to device + add to reading list' Action Chain so I'm thinking I might be better off disabling the split entirely - especially since
most books split as intended instead of having a single 500-page HTML file that freezes my Kobo.