Most of that sounded like a database corruption on one or both of the devices. Losing the reading position on sideloaded books and needing to redownload purchased books is a sign of this. If it had just been the Kobo Plus book, it might have been a sync issue that might have been fixed using the account repair.
Another possibility is the time on the two devices. If these were different, or the timezone was different, it could cause the problems with the syncing. When a sync happens, the status from the most recent action is taken. Differences in times on the devices could explain the weirdness of the Kobo Plus book.
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