What if each team is awarded a point every time an opponent's flag is captured. Then for example, the blue team would retrieve the flag from the red teams box (this also confirms the point) and put it back into play. This way flags would remain in play and more flags might not be needed. The winner of the game would be the one with the most points at the end of the period – 10 days, 1 month, whatever.
My thought is to keep flags in play so there is plenty opportunity for action.