A reflash will wipe everything on the internal flash and leave you with a clean slate. If a reflash doesn't fix something it would point strongly to the problem being a hardware issue (which is probably not the case here) or maybe something with the bootloader (again, obviously not the case here). Also, be wary of magic::sys or whatever it's called while in red pill mode. Trying to upgrade that is asking for trouble from what I've heard. If you do manage to figure out what went wrong before you reflash do tell us though. I'm curious.

-John