Let me give an example to see if I understand the limitations correctly.
If I have a palm tree currently set on Channel 3 on my 1st Lynx Express (overall system channel 3), and I physically change my extension cord routing and hardware to have it run to Channel 4 on my 2nd Lynx Express (overall system channel 20), is there no quick way to change the Vixen software (on Vixen 2.0) to move my channel order to reflect this hardware change? i.e. move the palm tree from channel 3 to channel 20?
Given your more detailed explanation of what it is you want to do, then:
1) I answered the correct question
2) I believe I answered the question correctly
Unless someone corrects me because I am wrong (which is always likely), the only thing you can do is (assuming you are swapping channels 3 and 20):
1) right click on channel 3
2) Copy the channel
3) paste it to an empty channel (one you are not using - say channel 100)
4) right click on Channel 20
5) Copy the channel
6) paste it into channel 3
7) Copy channel 100

Paste it into channel 20
9) Clear channel 100
I am not aware of remapping channels in Vixen to different output channels in the yard. In fact, in one of the other Christmas light forums, a similar discussion just happened. Someone thought it was possible (feature added) but they cannot figure it out. I think he was thinking about Vixen+ or Vixen 3.
5)