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I'm having the same problem but I have books that I bought from W H Smiths in my library under the 'I'm reading' tab but they are not in my purchased tab so If you delete them on the Kobo Glo they get removed from Kobo Desktop and my Library. When I search for a book I've deleted on Kobobooks.com I can still download them but they are not in my library but Kobobooks.com still thinks its in my library. Anyway I have decided to make another Kobo account and use that one for syncing as there's no books in my second account and updating. Then I just download the epubs from kobobooks.com and sideload them with calibre.
I hope Kobo does a fix for this as its a massive headache trying to only sync certain books at the moment.
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