Well, I did have to sync my libraries, and lost the 'mystery' books.
It appears
Web library > desktop library; any extra books in desktop deleted on sync.
Web library (via desktop) > e-reader library. the books are not taken from desktop to the e-reader, but downloaded again for the e-reader (so equal to syncing over WiFi). Again any extra books are deleted.
I did not work out how to backup the e-reader's books.
thanks for pointing me to the apprentice, interesting, but I couldn't work out what the keys on the e-reader are.
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