I suspect the fix will be to do a factory reset. This won't change the size of the partition but it will rebuild it. But, you can try something:
If just the configuration is being lost, the "Kobo eReader.conf" isn't being saved each time. Do a checkdisk to make sure the files system is OK.
Or, if it is asking you to login each time, then the database is corrupt. After logging in, do a log out. That will force a new database to be created.
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