So yesterday I finally got into the game and saw the Co-Op commander level issue. Figuring it would be a while to before it was fixed I went into a challenge in the campaign mode to try and improve my knowledge of the game. And anyway when I came back, all of my Co-Op commander levels were restored. I tried it again today since it happened again. It worked again.
So I’m not sure if this will work for everyone but try loading up a campaign mission (you don’t have to actually play it. I tested this the second time to be sure.) and when you come back to the main menu check your co-op commanders. You will also need to do this every time you launch the game or presumably log in.
This seems to be some issue with the servers being unable to recognize things. not sure why though. At any rate, I’m curious to see if this works or not for other people. If it does cool. If not, maybe I just got lucky. I honestly don’t know.