It's fact that Marco flames heal.
The main purpose to using his flames was to suppress the virus but that doesn't stop it from healing the people hit by his flames.
Chopper wants to heal everyone infected, friend or for. He told everyone to heat up their bodies to suppress the virus. Marco then used his flames on Chpper to show him he could help.
Next he used a huge fire attack on the area to suppress the infected people's virus. Remember, they weren't location at any certain area but everywhere. So Marco needed a large enough attack to make sure everyone infected was hit. Hitting a none infected person does not harm them but missing an infected people would put them back at square one and cause the virus to run rampage again.
Understand, the scene doesn't show the full size of the attack.
Apoo was in the middle of the area that was hit so he would have been hit by the flames and healed/revived some. The flames have limited healing powers on people.
The flames only continue to burn the infected area. Chopper whole body was on fire but the part that continue to burn was only the infected part.
Shortly after Marco use his flames we see Apoo get up. Still weaken but up.
This page also shows the following:
- Chopper infected side is the part of his body that is still burning
- it further proves Apoo was KO and was just revived because the first thing he does was try to get the antidote back. If he was conscious earlier he would have tried to get the antidote sooner.