There is no need to change the output source settings when the fx loop is active. When the loop is active the signal that is present at the direct out is determined by the position of the loop. If you want to send just the naked guitar signal after it has passed the AD conversion you should simply place the fx loop in Stomp A. This is exactly what the Git/processing output source delivers. To get the most out of a 4 cable setup stomp D is the perfect spot for the FX loop as I already explained in my previous post.
Hm. Understood, I'll get working on it next time I'm at the studio. Thanks for your help!