Robert, can you recreate the situation in Step 4 of your steps from earlier, and PM me the books.db?
Ideally, I'd like to get two copies:
1) Before you unplug the device, after say, quitting Calibre to make sure it has written everything out to the file.
2) After letting the T1 remove books from the collections, connecting the T1, and not using Calibre again.
#1 will give me the state that Calibre set.
#2 will give me the state that the T1 corrected it to.
I should be able to figure out what is likely going wrong at that point.
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