I had both the auto-sync issue and the continuous sync issue. Added the PeriodicAutoSync=false line to the conf file and was able to disable auto-sync. Device was still trying to sync continuously. Rebooted. Device was not trying to sync continuously, but when I tried a manual sync, it never completed and was stuck trying to sync continuously again. Signed out of account and back in. Added PeriodicAutoSync=false line again. Have manually synced around 12 times since and continuous sync problem has not reoccurred. Tested with both sideloaded books only and mixture of sideloaded and Kobo-purchased books. Device currently drains maybe 1% overnight.
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