Is it the rule that you must discard the rest of your hand if you have no more encounter cards that keeps the flares in constant circulation?
Otherwise I assume if you have some means of keeping your hand full (ie lots of compensations or rewards) you could keep a flare in your hand the entire game thus preventing its native host from being able to use it.
I suppose you could also take it from someone via compensation...
Right. There are also some aliens that let you screw with people's hands (like Barbarian). A few artifacts also require flares to be discarded I think. And you'd be surprised how easy it is to get rid of someone's flare if everybody works together!