Hi folks ... very interesting comments. I was educated in the Navy in electronics and have spent 25 years in the industry (Video Industry to be specific). Many of you are correct as there is no full proof method of protection from lightning. The best you can hope for is to disconnect all equipment from source for complete isolation. The Axe-FX was part of my studio and not used in a stand alone manner.
Because of the interest and comments assuming the surge came from the power side, I will add a few comments about how I was using the gear at the time of the strike. See below for those interested. Thanks for the comments and conversation! The unit has been shipped back to Fractal so will be curious to find out the true issue in a few days!
I wasn't playing at the time. The unit was fully wired into my studio utilizing most of the inputs/outputs, but no active signal at time of surge. I did have an Axe-Edit session active via a Mac Book Air, USB cable to Axe obviously. The power supply to the Mac Book Air was fried, the Mac Book Air was put into a battery drained state (I'll explain) and this is when; after I turned the breakers back on and powered the studio back up, discovered the Axe-FX with all LED's lit along with the bypass and tempo lights. Via web forums, I was able to fix the Mac Book by disconnecting / reconnecting the battery cable and that restored normal operations to the computer.
I believe the damage came via the USB cable vs. the power input. I've later discovered the XLR ports on my mixer coming from the Axe-FX are now damaged as well. Being that the Axe can be used as an Audio Interface, one might assume these two could be part of the same circuitry. Will be interesting to see the findings. Curious to hear your feedback!