OK, from looking at the instruction manual for bot the AT-9 and the WB68 I don't see anywhere that it says a specific cable from the AT-9 MUST go to a specific port on the WB68.
On the AT-9 there are two LNB assemblies on it, one for 99/101/103 and the second for 110/119, see
http://www.solidsignal.com/manuals/AT9_install_manual.pdf
On the WB68's instructions at
http://www.hometech.com/pdf/gc-wb68.pdf on page 7 it says just hook for lines from the AT-9 to the WB68, doesn't say a specific cable needs to go to a specific port on the WB68. I've had two of these things installed and the installed didn't mark any cables or ton out which was which, just connected all four cables.
Now if you disconnect one of the cable yep you're going to be loosing some channels. If D* is doing the same thing with this new dish and switch you're probably loosing either horizontal or vertical polarization transponders from either the Ka or Ku band satellites.