I encountered a missing NETLOGON folder during a domain controller replacement. I was able to rebuild the NETLOGON folder by setting a single registry value. The full scenario is as follows:
DC05 = Old Domain Controller
DC232 = New Replacement Domain Controller
DC01 = Domain Controller
DC232 was promoted to a DC, before it completely finished replication DC05 was demoted and turned off. DC232 was then missing its NETLOGON folder. Event 13565 appeared in the File Replication Service log in Event Viewer. To correct this problem the following registry key needed to be changed:
HKLM\SYSTEM\CurrentControlSet\Services\NtFrs\Parameters\SysVol Seeding\Domain System Volume (SYSVOL share)\Replica Set Parent
In this case it was set to the recently demoted and now unavailable \\dc05.contoso.com Changed the value to \\dc01.contoso.com and restarted the NETLOGON and File Replication Services. Once replication was complete event 13516 appeared and the NETLOGON share was created.