With my first pregnancy I kept mine in all the way but did put a normal ear sleeper in towards the end just for comfort as that sat flat & didn't rub on clothes etc.
With my second I took it out around 30 weeks I think with the intention of putting the sleeper in again but I never got around to doing it.
With both pregnancys I had comments from Ob & M/W about how I would have to take that out soon. But I didn't see the need. I had no problem what so ever with the hole closing. I have had mine pirced for about 6 or so years so maybe thats why. But I don't think its like your ears I can't see it healing over?