I haven't had any issues sideloading epubs to any of the recent Kobo firmware or with any recent calibre version or combination.
A corrupt database could be a reason. Calibre can show an error when the device was connected if the database is corrupted, but that will depend on the tables that are corrupt. My Kobo Utilities has a database check function that does a thorough check. If it returns OK, then the database is OK.
If it is corrupt, you don't need to do a factory reset. Sign out of the Kobo account first. The database will be recreated when you sign in again and the sideloaded books reloaded. If that doesn't work, then you can go to the factory reset.
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