If you want to test whether the internal micro SD card is the problem, it is (or was) possible to boot the Kobo from an external card. I haven't done it, except to try Android once, and that wasn't very nice. Google is your friend.
Copy a factory ROM to the external card, do whatever voodoo magic is required to get the Kobo to boot from the external card, and see if that solves the problem. At least, that's the theory.
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