Deleting an Organization VDC that has shared networks in use by one or more Organization VDC's will remove the shared networks from any vApps that use these networks. This will also leave the NIC's attached to the VM in a disconnected state in VMware Cloud Director.
VMware Cloud Director 10.x
This is expected behaviour as deleting an Organization VDC will remove all resources connected to the Organization VDC including the shared networks.
To avoid running into this issue it is recommend to use Datacenter groups as the group is the owner of the shared networks and not the Organization VDC.
Create a Data Center Group with an NSX Network Provider Type
https://techdocs.broadcom.com/us/en/vmware-cis/cloud-director/vmware-cloud-director/10-6/map-for-vmware-cloud-director-tenant-portal-guide-10-6/working-with-networks-tenant/managing-data-center-groups-and-networks-backed-by-nsx-t-tenant/managing-nsx-t-data-center-groups-tenant/managing-nsx-t-data-center-groups-tenant.html