For those worrying about Flagship Check-In, do not fear.
I've literally just left JFK but had a long chat.with the staff.
The desks will be moving literally one row over from where they are now, and there will be a separate line which will meander you to the front of TSA Pre.
The staff have been told they're moving in mid February, but that keeps being delayed. The area won't necessarily be as hidden as it currently is, but the desk staff did stress it's obviously just a temporary move.
I've got quite a few trips through JFK over the next month, so it'll be interesting to see if they keep to the timeline.
I'm back through on Saturday, so happy to ask any questions people have.
M