moab
Inspired
One way to greatly minimize this especially with time based effects (delay,reverb) is make a general big rig patch with all the effects you'll need. Turn on "ignore redundant PC" in the midi section(Axe-Fx) and make sure your midi pedal is transmitting instant access states when changing programs. Next, program your midi pedal to store a "dry" state of the program with none of the instant access switches on. Then make a new preset on your midi pedal and program to access the same patch in the Axe-Fx with the instant access switches on (reverb, boost, delay, chorus, drive, X/Y, etc). Make sure the bypass mode in the delays and or reverbs are set to mute fx input. You should have no dropouts and the delay reverb tails will ring out switch between the two presets on your midi controller.