Sounds like a pretty frustrating experience Marcardis. I would like to try and help.
Please send me a screenshot of your library on the Desktop application if you don't mind. Please forward to shasan at kobo dot com.
Also, from the Library screen on the desktop app, please press CTRL+SHIFT+I. This will create a logfile called kobo-logfile.txt and drop it on your Windows desktop. Please send me this file as well.
I'm in transit most of tomorrow, but I will be checking email and will be online whenever I'm not in the air. Looking forward to working this out for you.
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