ASH,
There is a known issue with certain kinds of progress being lost. Are you running into issues with your commander levels being reset? If so, this may be relevant: [Main Thread] - Commander Levels Reset - #131 by Kaldraydis
If that’s not what you’re experiencing, you may want to see if your progress returns once the game is able to sync your cloud data down from Battle.net.
EDIT: I originally posted an old thread that is being redirected. I have updated the link to the recommended thread.