If an obscene unit is compelled to retreat twice in in one combat, he receives two flags at once, does he still get to counter before he retreats? Can he counter twice?

You're allowed to counter before retreating; "retreat" implies moving in an opposite direction for X hexes, where X = to the number of flags rolled. So:

a) yes, you can counter regardless of the number of flags

b) you can counter only once (it's the fact that you retreat, not how much you retreat)