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I'm trying to work out what your saying you've done.
1) Are you saying Calibre has been populated by the books from your three kindles? I.e you dragged them from Calibre somehow into the library.
2) Or did you have a pre populated Calibre and the books on your Paperwhite aren't showing as ticked when they are on the device?
I can't imagine how you could have done number 1 tbh.
Number 2 happens when the books on your kindle are downloaded from the Amazon cloud but when you loaded them in Calibre the name has been altered in some way. I don't use Calibre with the kindle but when I have occasionally connected it the tick marks never match.
Either way I think a mod should move this thread to the Calibre devices forum as you need help from the Calibre people.
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