Try going into the antenna setup on the HR2x, select "Reset Settings" to wipe the current db, then redo the "Initial Setup", it may help if the changes have already been mapped to the DirecTV database.
I had a problem with 2 of my locals swapping: ch 26 and 38 shared a transmitter, but on the 12th 26 moved to its original frequency when they turned analog off - ch 38 went from 15-2 to 15-1 and ch 26 went from 15-1 to 26-1. Redoing everything fixed my problem.
Well, I did as you suggested and now it's worse. After issuing the Reset Settings and then doing the scan the Option to edit the Local channels is grayed out. Tried several times; same thing. Now no locals at all.