This is the intended behavior of the inputs. You can't save the setting in the Rig. To achieve what you're looking for, you need something like a Lehle box in front of the Kemper.
I personally just use cables with a Neutrik Silent Plug, or multiple wireless senders if it's a bigger show.
I thought this might be the case but just wanted to double check. I suppose its no big deal to switch the cables so I'll go with that, Thank you