I ran into the same issue with a different model, exact same symptoms and missing fields in mongodb.
I ran 'db.modelEntityRefs.update({_id: "13c240e8-04a7-4ae0-8568-d3fdbfd6cf72"}, { $set: { "volumes": [], "filesystems": [] }})', and after those volumes and filesystems fields were added, the modelEntityRefs documet for the model in question showed them and I could then delete it.
I ran into the same issue with a different model, exact same symptoms and missing fields in mongodb.
I ran 'db.modelEntity Refs.update( {_id: "13c240e8- 04a7-4ae0- 8568-d3fdbfd6cf 72"}, { $set: { "volumes": [], "filesystems": [] }})', and after those volumes and filesystems fields were added, the modelEntityRefs documet for the model in question showed them and I could then delete it.