Had this come up last night and we didn't know the correct answer.

Bossk is shooting Cluster Missiles and uses 4-Lom to deny the defender use of his focus token. Does this denial carry thought both instances of the Cluster Missile attack or just the first?

Just the first. He has to use 4LOM twice to block the token for both attacks, deciding independently for each attack.

The key is that 4-LOM says "during this attack", and Cluster Missiles are two attacks.