Well, that particular time I hadn't, but let's check that.…
Oh, that's embarassing
You're completely right.
That does however lead to the question: why do
deletes happen immediately, and
adds happen only when you disconnect the USB?
I think I know the answer, but it leads me to suspect the plugin is misbehaving. When I delete a book, I see the plugin issue the SQL to clean up the database, but surely if you
just delete the book, it will get cleaned up by the Kobo when I unplug the USB. And that way, there's a chance that restoring a bookmark may actually work without cycling the USB (not, of course, if changes to the driver settings or a manual request to store to a different card result in the filename changing).