FRS not replicating C:\WINDOWS\SYSVOL\domain\scripts after non-authoritative restore

The Problem happened again on another DC. It turns out that a few files were in the C:\Windows\Sysvol\domain\scripts folder - some exe files running. NTFRs.exe couldn't complete its task.

ntrfsutl was useful to debug this problem. http://support.microsoft.com/kb/822300/en-us is a certainly helpful. I used ntrfsutl inlog to see the state of files being transfered. For my case, the scripts folder was in state IBCO_INSTALL_REN_RETRY all the time. I then located all the files which held locks in the script directory (and its sub directories). Those were a few programs which were also running on client computers (but opened over the NETLOGON share).

You can use handles.exe from SysInternal Tools to identify open file handles. In my case some files were opened by the "System" process. Those were actually opened over the network share by client computers. I closed their handle via compmgmt.msc.

After all opened handles were closed, the replication finally succeeded.