I have been informed by Aegean's phone agents in the past that "double bookings" are eventually picked up by their system (so presumably some time before check-in opens) and that this will lead to a cancellation of one of the bookings (of course don't take this as a guarantee that not both bookings will be cancelled). I did this once too (I don't remember the exact circumstances, if one award and one paid ticket were involved or something else, but it was definitely for cost reasons, either in €€ or in miles), that's when I called to ask what would happen, so I subsequently changed (or cancelled, lol, sorry, that was some time ago!) the one I didn't want to keep immediately after that (so that the system wouldn't cancel the one I wanted to keep).