Hello @georgeb , after talking with Databricks team, I was able to grant and remove the access again. What they suggested was to add momentarily the user to the workspace that he's not part, remove the access from the application and then remove the user from the workspace permissions. 

In this way, I was able to grant access to new groups and removing the existing ones. Before that, the permission control broke and I was unable to remove or grant permissions. Hope this works for you as well 😀