My opponent has a fossil Zapdos, and he uses Thunderstorm. He has 7 damage
counters on it. I have a full bench. He flips 2 heads, a tails, then 2 heads.
Would he get knocked out when he flips tails, not doing 20 each to the last 2
pokemon, or would he?

Damage is not applied until all the coin flips are complete, so Zapdos would still get to flip for everyone.

Scott