The reauthorization warning is harmless. It's just notifying you that your non-commercial licenses will need to be reactivated soon. They don't need to be reactivated right away, though. Two weeks before non-commercial licenses are about to expire, houdini and mantra will warn you. Once they've expired, you only need to reactivate them once, and they'll be valid for another 30 days.
If you try to activate a license and a non-commercial license already exists for your computer, the same license keys will be returned. So, when you tried to install licenses manually, you were installing the same licenses that were already installed, as the error messages implied.
Removing the licenses file and reinstalling the licenses won't get rid of the messages, because the
licenses you're installing will expire in less than 14 days.
Sorry about the annoying messages.