Hunted shot, Twin takedown and Flurry of blows basically work the same: 2 attacks for 1 action and damage is combined for the purpose of resistances and weaknesses.
While you are hidden, target is flat-footed for the first attack: "If you attempt to Strike a creature, the creature remains flatfooted against that attack, and you then become observed."
The question is: Does flat-footed condition apply to both attacks or just the first one?