I have been struggling with this with an 7CM set up with my helix rack and two Mesa combos. One combo has simple single channel switching so I was able to use the CV output jack and transistor gate as mentioned in a number of other threads here.
The other combo has 3 channels toggled by the connection of Tip or Ring to ground, and this was the source of the ground loop issue. I built a pass through box with an isolated stereo jack on either side and then wired tip to tip and ring to ring from one jack to the other but I did not connect the sleeve terminals. The input came from the Ext Amp 1/2 jack and the output went to the combo channel switching jack. Once I put this box in the channel switching path, it complete resolve the sound loop issue and I can run both amps (and control them) from the helix with no issues.