My Co-Op commander progress was reset as well. I have attempted every single suggested fix in the forums, especially all of those suggested by Blizzard. I just absolutely can not get my progress back no matter what I do. I have even given it several days, weeks, to see if perhaps it just straightens itself out on server end with no luck.
I tried region changing, signing in and out, assuring that I am on the correct account, running the game as administrator, reinstalling, and every other suggested fix out there.