He could have been doing a number other things like gathering up the samurais they captured in the capital. Or Even chilling with the other flying six. Just because we didn't see him it's not proof he was knocked out.
If Oda wanted to show us that Sanji knocked him out or put him in a coma he would have showed it.
If Oda wanted to show us that Sanji knocked him out or put him in a coma he would have showed it.