Gave it two more tries.
First try was the same as above, only ejecting through Calibre. It briefly showed the books, before they disappeared one by one.
Second try as the one above up and including step 4, only then:
5. Open Calibre
6. Send books to device
7. Eject
8. Importing books
So far it seems to keep the books and status. I don't have any more time, but I'll add some more books later and see if it resets everything again.
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