Archfiend of Despair’s last ability counts only how much life was lost. It doesn’t care whether a player also gained life.

In a Two-Headed Giant game, damage and life loss happen to each player individually. If each player on a team is dealt 2 damage, each of those players loses 2 life and the team’s life total goes down by 4. When Archfiend of Despair’s ability resolves, each of those players again loses 2 life and the team’s life total goes down again by 4; they don’t each lose 4 life.

The amount of life to lose is determined only as Archfiend of Despair’s triggered ability resolves. For example, if you control two of them and an opponent lost 3 life earlier in the turn, the first ability to resolve would have that player lose 3 life, and the second would have that player lose 6 life.