When running 44 or 42 etc. switches, we always use individual DP Lnbs with a "W" bracket. Higher gain and less prone to issues.Honestly until dish starts switching back to a dual lnb I would keep the third line connected on a 44 switch. The ports on lnb aren't really assigned a specific satellite bit since it's a triple lnb when connected to a switch it's going to try all three satellites, even if the 129 is no longer active with only 2/3 cables connected it could cause issues. I don't believe we've gotten any official word from dish on how to handle switches since the change but I'd keep all three lines connected.
We recently had to travel to all our Smart Box accts, about 30 of them over 2 states (Washington and Oregon), and reprogram them to remove 129. Dish recommended physically disconnecting the 129 feed also, and on 211Ks. (We sometimes run a half dozen 211Ks with our Smart Box to handle music channels.)