Okay hang on this is making sense to me.
@michaelson is saying that if your newest update gets very popular very fast, it is technically possible to be in fresh and popular at the same time.
But you are correct in your observation that updating bumps your comic out of popular.
The reason isn't "you can't be in fresh & popular simultaneously," it's that Popular apparently only samples your newest episode. So when you update, no one has interacted with the newest episode, so the system sees it as "no longer popular" and you get knocked out of the Popular section until people interact with the new one.
Am I understanding this?