Yes we have done this so have not had to change rooms. Just put a note in advance for the room controller as continuing and go to the front desk 1st thing in the morning for the change over to be completed.
I never knew that there are dedicated 2 bedrooms at BWV, great info.
The other thing I did at Boardwalk was to ask for a dedicated room on our first reservation, so that it wouldn't matter to any other reservation on the change over day. If you were in "half" of a lock off room you might have to move to accommodate someone else's reservatIon, depends on who is checking-in-and-out that day.