Question: will the second signal (which is isolated on the way in) still be isolated as output 2 from the H9 or do I need to isolate it again using a lehle psplit before sending it to the second amp?
You will need to isolate again because isolation has to do with ground loops in the system, and since you’re introducing the H9 after the original isolated point, there’s risk the pedal’s electronics couple the electricity again.
Question: the G3s also has the functionality to reverse the phase on the second output if I encounter phase problems. Will that functionality be maintained as the signal passes through the H9?
Yes, but you have to be careful with reversing the phase too early in the signal chain as that can interfere with how the algorithms process the signal. Like decoupling, I would recommend flipping the phase post H9 as well.