If the Multi-VC VM is deleted directly from disk or from vCenter Server B, the deletion operation also removes the VMX and VMDK files of the original source VM template. This occurs because the Multi-VC VM spans both vCenter Server instances but references the same underlying files as the source template on shared storage.
VMware Cloud Director 10.x
This issue is caused as the multi-vc-vm has the same VMDK as the source VM, deleting the multi_vc_vm, also deletes the vmdk for the source vm. Hence deleting this from vCenter is not Ideal.
To safely delete Multi-VC VMs, use VMware Cloud Director APIs instead of deleting them directly from vCenter.
Reference: https://developer.broadcom.com/xapis/vmware-cloud-director-openapi/latest/multi-vc-vms/
Step 1: Retrieve Multi-VC VM IDs
Step 2: Unregister the Multi-VC VM
Please note: