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Thanks guys for the quick reactions.
@eschwartz: I could not find the collections on my PW, nor on the my Amazon account. But they were visible on my, almost never used, phone app. When I deleted them on the phone I could manage them on the PW. That is weird, there obviously is syncing between the devices but not always.
So the collection problem is gone
@Dr. Drib:
I did not use Calibre for the adding and removing. I simply used Windows Explorer. The strange thing was that when I removed a book, including, the extra files generated by the Kindle it stayed visible in the library. I could not open it of course, but deleting was also not possible. When I re-added the book it showed up twice. The factory reset took care of that.
At this moment I have a fully functioning Kindle with a correct library. As I'm leaving for a 5 week vacation tomorrow, I will leave it this way. To little time and when not broke, don't fix it
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