That's the problem with hacks... yes, there may be issues, since CB works based on the Joomla framework, so changes to Joomla will likely have unexpected results. You may need to sync users manually and have other problems... or maybe it will be fine as long as you use the CB login module and registration.
I'm interested to hear your results. Hopefully, the choice will again be part of the Joomla core. I don't remember which email/usernames I use sometimes!