From the rulebook "Any conditions that the attacker gained as a result of the defender’s damage barrier or counterstrike, if they have “end of Action Phase” effects, are not resolved at the end of this Action Phase. For example, if the defender Stunned the attacker with his damage barrier, leave the Stun marker on the attacker and do not remove it at the end of this Action Phase. In this manner it will remain in play and will have an effect on the attacker for his next Action Phase."
In short, no, they stay on.