Many thanks for your suggestions! I did double check now and I don't have two copies of the same book on the T1. The other thing is that all my book have duplicated highlights (at least all the ones I sync'd), so it's not an isolated case. I can see duplicated highlights both on the T1 and on my Mac.
So you are suggesting deleting books.db on the T1. Will I not loose all my highlights and so on?
Should I then restart the T1?
And/Or
Should I sync it with the Mac App?
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