I had the exact same problem starting today. Found the solution here: https://developercommunity.microsoft.com/t/My-Git-repos-suddenly-disappeared/11078522?sort=newest
- In "Organization Settings" > "Users", look at "Access Level" for the affected users. In my case it was "Visual Studio Enterprise subscription", with a warning icon and tooltip that said "Subscription expired" (I've never had a full blown subscription with this organization so dunno what happened)
- Click on "..." at the end of the user's line, then "Change access level", and change it from "Visual Studio Enterprise subscription" to "Basic", then Save
- In my case at least, repos are back in the portal, and they work again from the command line. Yeah!