If you are referring to NSX-v, there is no clustering concept for NSX Managers . Primary and Secondary NSX is primarily for Multisite/Cross site deployments and not to protect a single site NSX deployments.  However in NSX-T we can deploy a 3 Node NSX Manager cluster which makes sense since it is a collapsed management/control plane cluster.

If you have any sort of corruption or unrecoverable file-system issues , restoring from backup is the last option(If VMware support can't fix it). Please don't be too much concerned about this , its a very rare chance but regular backup and monitoring should be in place.