Actually, as I mentioned before, the three merchant brothers are seen after the ending to the game's 2.0 storyline at the Waking Sands alive and well, congratulating the player for
taking down Gaius and the Garleans.
But yes they're not seen again so their current (post Operation Archon) whereabouts are unknown. But given the fact they're merchants, they're probably out on the road hawking their wares most likely.