I opened a trouble ticket with Kobo with regards to the deleted html files still showing up in the Documents list, and their somewhat-helpful suggestion is copied below:
You may have a corrupted database. Try a factory reset (menu-settings-advanced settings-factory reset) but we should warn you that this will clean our your ereader and you will have to reload everything.
I didn't want to do anything quite so drastic if it wasn't actually necessary, and my Kobo was otherwise fully functional and working just fine. As some kind soul posted upthread:
Originally Posted by timlegge
The most recent version of Calibre should allow you to delete the HTML and txt docs
I finally had opportunity to try this today. I can confirm that using Calibre to remove the "ghost" entries from the database appears to work fine, and my Kobo isn't showing any other problematic symptoms. I:
1) plugged in my Kobo
2) started Calibre
3) selected "Show books in the main memory of the device"
4) highlighted ONLY the html files I'd previously deleted from the Kobo, but which were still showing in the device's Documents list
5) pressed the Delete key, and waited for it to finish
6) ejected the Kobo
In other words, the problem was NOT that the Kobo database was corrupt. The problem must have been that the Kobo simply doesn't remove the database entries when html files are removed from the device.
So hopefully this relatively minor issue will be corrected with a future firmware update, and others having the same problem can be given a solution other than "wipe it and start over". ;-)