The presets that I created did not change tone at all from the upgrade. either you have done something very different than what I do in my presets or you have not gone back to your global settings and adjusted them from the defaults that were loaded after the mandatory reset with switches 9 and 10, or you did put your IRs back in the proper location.
Would you upgrade Windows on your computer the night before a big presentation? The Helix is basically a computer running software, treat it like one.
-Max