You cannot find a host in the SDDC manager inventory, acompanied by the NSX error message:
There are hosts in this NSX that are not known to SDDC Manager
and the host does not appear in the SDDC manager database. Check if the host appears in the SDDC database using the following commands:
$ psql --host=localhost -U postgres -d platform
$ select id, hostname, status from host where hostname='<ESXI_HOST_FQDN>';
If that final command does not produce an output containing the host in question, your host is absent from the DB.
SDDC Manager 5.2.x
The host has been removed from the SDDC manager database.
You must decomission the host from your VCF environment, remove it from inventory within vSphere, re-image it, and add it back to your VCF environment.