Now, I'm no expert, but as far as I know, lower impedance muffles the sound of the guitar, making it less bright, and lowers the signal level. So I think there's some sort of impedance confusion going on here. Set the input impedance on your Helix to Auto and try it like that. Also, when you do A/B the pedals, use as simple a preset as possible. Just the pedal and amp. And if you're using a real pedal in the send loop of the Helix, I am not sure how impedance is handled in that case. It may very well be that mismatched impedance is the root cause here.