If FQDN is used as "Object Manager Display Name" and "Web Host" and a server host name is used as "Primary Server Node" during pdm_configure in CA SDM r12.5 or earlier, two servers are added automatically under ADMINISTRATION->System->Servers after CA SDM is migrated to r12.9.
This is working by design.
The design of the CA SDM Repository function was changed starting in CA SDM 12.9. If the server name specified as Servlet path is not found within the usp_servers MDB table and is subjected to an upgrade to CA SDM 12.9, the server name will be added as a dummy secondary server to usp_servers MDB table.
The added dummy secondary server will not impact existing functionality as long as it is inactive. However, if you change the server (machine) name to FQDN, it might impact CA SDM as it is already within the usp_server MDB table.
In order to avoid the dummy server from being added automatically, change the Servlet path from FQDN to a host name before the CA SDM migration.
If you would like to use FQDN as the Servlet Path, please apply the r12.9 Cumulative #1 patch and then specify the FQDN in the Servlet Path field in the Server setting.