Thanks, seems we're thinking on the same lines.
I tried Alt-Del yesterday just in case. It shouldn't make any difference, and it didn't.
Regarding (ii), it's hard to see how a backup program on my PC can mysteriously put the files back on the Kindle after it's been disconnected from it.
However, I agree that it's good to eliminate variables, so I tried the same routine on a laptop that has never seen any Kindle before. Same result.
Here's an idea. When files are deleted, they don't get wiped right away, just tagged as deleted. Could be that the Kindle is detecting an error with the disk at startup, and in trying to fix the error, is undeleting all the recently deleted files?
If so, formatting the drive is the obvious answer, but I don't know enough about Kindles to say whether that's a safe thing to try. Can anyone advise?
Thanks!