Thanks for the info, Peter. No criticism of it implied, but I don't personally like the way Calibre restructures and manages your file storage. I understand why it does it - well, a basic understanding, anyway - but I still don't care for it.
Meantime, I've discovered the metadata editor in Sigil, and have confirmed that the metadata is what the KT is reading in the files to construct the Library menu, so it's easy enough to fix - though of course it means DRM has to go out the window. (I don't have any qualms about that; I don't distribute files, so I figure I'm still abiding by at least the principle of DRM.)
I've discovered a peculiarity in the KT's database, though. I tried amending the metadata in a few errant files and replacing the copies already on the KT with the updated ones, but even though the KT recognised the files had changed and went through the "updating content" process when I disconnected it, the subsequent menu still used the cached info of the previous copies of the files. I'm sure there's a database file I could have deleted that would force the KT to rebuild it with new data, but I wasn't sure which one that would be. (I suspect it would be the KoboReader.sqlite file in the kobo directory, but I hesitated at simply removing any of the OS files.)
The only way I found to force the menu to update was to remove the book files, then the USB connection, let the system rebuild the menu without those books, then reconnect it, copy the new files on and let it rebuild the menu again.
A bit of a shortcoming in the menuing system, I think. And yes, I'm using the latest firmware (.16).
Anyway, now I know I need to check metadata on book files before I copy them onto the KT.