The NSX Controller Nodes do not need to be backed up, as they retrieve the configuration from NSX Manager. In the case where NSX controllers were deleted, are missing from the configuration/UI, failed to re-join the cluster, or we are experiencing multiple controller failure, the NSX Controller Nodes can be restored by redeploying a new set of NSX Controller Nodes.
The supported procedure to redeploy NSX Controller Nodes is to delete all three existing controller nodes, deploy three new controller nodes, and perform a controller state update.