Possibly not. It is called a multi-switch not a voltage switch. The one you are using is passive as it uses the ird's voltage to switch instead of an external PS. Like Larry said on long runs a powered switch is always better but once again this may not be your problem. The 2 lnb's are looking at 2 different birds. If you have a bad LNB on the 101 side it will not effect the HD channels. What we were talking about sides in reference to a dual LNB was a 14 volt side and an 18 volt side but both coming out of the same LNB. If you have an LNB problem and you swapped LNB's at the dish then yes if the LNB was bad then you would have problems with the HD channels if it originally was bad on the 101 side but just swapping the wires will only change which channels or I should say transponders are effected from the same LNB unless of course if you have a bad wire.
Here is what you can do. If it happens again have the custy go into the setup menu and see which tranponders aren't getting signal odds or even's. If you swap the wires and the opposite channels don't work the you have isolated the bad side so it could only be the lnb or the wire from that side. If the channels didn't change after switching wires then I would look at the mulitswitch and also check the voltage out of both ird's make sure they are both switching.
