Problem persists. Looking at the Nook when mounted on the Mac desktop as a drive, all the missing books are there, in folders by author, but the Nook doesn't show them as available.
I've also found a few dozen books that I can't sideload no matter what (from Calibre). Calibre claims they're successfully transferred, the Mac can see them on the desktop, but the Nook can't see them.
At this point, I just do a factory reset every so often and reload one or two books.
Alas, I'd imagined I could keep several dozen books on the Nook for traveling, but that's not going to work.
I'll look into
https://forum.xda-developers.com/nook-touch, thanks for the suggestion.