There may be GPOs listed in the Deleted Objects container within GPOAdmin that are still registered with the product but have been deleted natively; the GPO itself no longer exists.
GPOs exist as storage objects within the VCRoot container and are named with the GPOAdmin ID. It is possible to delete them from the VCRoot container, but the safer and preferred method is to unregister the GPO from the Deleted Objects (right-click on the GPO). You can sort the GPO's by domain and then unregister them. If you cannot unregister the GPOs, please try the following:
If you cannot delete the domain or the GPOs that no longer exist, you may need to delete the objects from VCRoot by searching for the GPOADmin GUID with a recursive query.