What do you mean by 'closing' the books on your Kobo?
Buying a book from Kobo on your phone (or other device) and then syncing to your Kobo reader should work. It sounds like something happened with that 'closing' causing your Kobo account to think those books were newly added to your account, and thus is synced them again. If you leave things as is now and just bring the books you're currently reading to the front of the my reading list (by opening them), syncs should't change anything anymore.
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