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Thanks for the advice. Generating a TOC from major headings (or headings at all) did not seem to work, but I used the option "Generate TOC from files", and that gave me something I could work with, after I removed some entries (all of the author blurbs were in standalone files). The "beautify HTML" option also un-flattened all of the core text and made it more readable.
Once I did those, the resulting EPUBs had a working ToC, and seemingly chapter markers as well: my Kobo detected chapters at each ToC point. Both books are looking great now.
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