Time will tell, but I think you will be ok. If scrims are up during a room refurbishment, they won’t be nearly as severe as the ones during the Copper Creek conversion. In that case, half of the lobby was closed off. In the upcoming refurbishment, only one floor will be closed off and the scrims will be much just on one floor, and likely not blocking the lobby rooms.
The fact that you have reservations for a bunk bed room sounds good. I highly doubt Disney will not be able to give you the room you have reserved, so I would keep the reservation and look forward to getting the bunk beds. If they are to be removed, that would most likely occur after your stay.
Happy planning and I hope you get to have a great trip.
I am sure the “upgrade” to a CCV room is optional. Some would love it, others not so much, and a lot of that is tied to whether you want a real second bed. It is interesting that some have gotten CCV rooms, but isn’t something I’d worry about if I didn’t want one.