Symptoms:
This issue occurs because the LogicalSwitchBulkMsg during transport node deletion did not reach the transport node or was not sent by management plane to transport node.
This issue is resolved in VMware NSX-T Data Center 3.0 and later, available at Broadcom Downloads.
Workaround:
If the segments were present and persist after upgrade, file a support request with VMware Support and quote this Knowledge Base article ID (76521) in the problem description. For more information, see How to Submit a Support Request.
The information about opaque networks are communicated to the vCenter Server from the ESXi hosts, so it must be the host who still have them in the case that they were not deleted correctly.
To check:
A similar check can be done in the host CLI looking at the proxy switch in there, if there are UUIDs on the property property ‘com.vmware.port.extraConfig.opaqueNetwork.id’, then you have still an N-VDS proxy switch, and logical switches in there:
For example:
[root@esxi:~] net-dvs -l | grep '.opaqueNetwork.id'
com.vmware.port.extraConfig.opaqueNetwork.id = , propType = CONFIG
com.vmware.port.extraConfig.opaqueNetwork.id = , propType = CONFIG
com.vmware.port.extraConfig.opaqueNetwork.id = 624ea4d1-ba56-4805-b244-ecc95ca0c2a1 , propType = CONFIG >>>>>>>>>>> This is a logical switch
Note: This would not show why the host still have the portgroups, but it will confirm that the problem is in the host as it is advertising those.