Oh oh, another unusual use-case! The users are so much more inventive than the test-case generators...
I really don't know how the authorizing of Kobo accounts is tied to the Adobe account, but I'm not too surprised that your use-case causes trouble. I'm sure they expected couples who share a single Kobo to share a single account, as well.
I'm not sure there is anything that can be done here except to contact Kobo's customer support and ask them to close one account and transfer its books over to the other account. But they may have other suggestions.