That should make no difference. You're deciding to change what's defined in a channel. If a channel is in use in a given scene, then it will use whatever you changed the channel settings to be.
No different than if you manually changed it.
Say I have 4 presets with increasing levels of gain 1-4.
But because of the way the preset evolved, the amp channels aren't A-B-C-D, they're D-B-C-A.
Works fine, but it's "out of order".
If you swap channels A and D and don't modify the scenes, the amp channels are in gain order now, but the scenes are messed up, in the sense that they're not in gain order any more, and any other blocks or settings that were supposed to go with the high- and low-gain channels you switched aren't with their intended amp channels.
That's option one for how swapping channels could work -- assume nothing else should change, which as a result changes the sound of the affected scenes.
Option two would be to assume that the tones are where you want them to be in each scene, you only want to swap which channels are labelled A and D.
To accomplish that, the swap action would have to swap the channel settings as above, and also adjust any scenes that used channel A to use channel D, and vice versa.
Net effect would be to swap the channels, but leave the sound of the scenes the same.
That second behavior is most commonly what I'm thinking of when I find myself want to swap channels.
