My understanding is that only one FF program can be associated with the ticket.
By having your Etihad Guest No on it, your "Etihad status" will be recorded on the passenger manifest. The only benefit of that apart from the miles is your status is listed against your name and may hold a better chance of an upgrade if there are to be any on the flights you're taking.

Lounge access is a given by presenting your Etihad Guest card at the Lounge reception but odds are they may add your guest no to your PNR at the same time.
The fact that your Guest No is already on the PNR may complicate the possibility of changing it to Velocity. Though they can add Guest Nos at check in, there should be no reason why they can't delete them also.