I think you accidentally fixed one of the problems. I suspect the sideloaded books not turning up and the syncing was because of a corrupt database on the device. The sign out and back in removed the corrupt database and created a new one.
The sign out and in also regenerated all the system files such as the affiliates file. You will need to change this again to get Pocket back. But, I suggest just "Kobo" for the affiliate.
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