I just wanted to update this post because the issue has been resolved.
Line 6 found that the issue could only be resolved with a simple internal mod. They rented a Friedman JJ100 in order to troubleshoot and find a fix. It took them awhile to get this all done, but they stuck to it. D.I. followed the whole process and kept me updated on a regular basis. At the end of the day, Line 6 stepped up to the plate and did what was right and resolved my issue. They have been a class act the whole time. Top notch!
Thanks again D.I.
To anyone that has a Friedman out there or will be getting one, this mod will need to be done to your Helix if you plan on using it to channel switch the amp.