I have the similar problem 1TB onedrive for business account with cloud drive set up for 800GB size. There has been deletions and additions to the drive and now the clouddrive shows 750gb populated and 50gb free space but the onedrive admin view shows that full 1TB has been utilized, there is nothing in primary or secondary recycle bin on onedrive to delete. It simply shows that clouddrive folder is occupying 1TB to storage. I have an issue now, I can't delete anything on the ondrive since nothing is available to delete, drive is maxed out so it is rejecting the API calls from cloud drive and my drive shows 50gb space. I have also raised a support request with stablebit but no info yet.