Time must have passed then. He opened a portal in the gaiden and when he came back he had to return and recharge. Or when they had a rest after they beat momoshiki seeing as they never returned straight away.
or you are speculating as is what you have been doing all this while. gaiden never showed him opening a portal and getting drained. he was already drained when we saw him meaning we dont know how many times he was able to use the portals that led him to such a state so saying he opens one portal and then needs a recharge is nothing speculation.Sasuke opened the portal and he didn't come to naruto's location straight away. Time passed (cool down time) that's why he still has the tomoes. Or the movies contradicting the manga
when he needs a recharge, he loses his EMS and its powers for a while yet we saw him use what looks like kagutusuchi chidori on his blade to cut kinishikis weapon not too long after opening the portal that took them there. that kagusuchi wouldnt be possible if he couldnt access his Ems powers.