We are running several Windows Server 2008 R2 domain controllers. The replication of sysvol is done by NTFRS.
Yesterday, our master DC reported a "JRNL_WRAP_ERROR" for the SYSVOL Share. I ran a chkdsk on C:\ but it did not show any problems. After this, I have initiated an non-authoritative restore by stopping ntfrs.exe, setting BurFlags to "D2" in HKLM/SYSTEM/CurrentControlSet/services/Ntfrs/Parameters/Backup\Restore/Process at Startup and restarting ntrfs.exe again.
While this seems to work for C:\WINDOWS\SYSVOL\domain\Policies, it for some reason does not pull C:\Windows\Sysvol\domain\scripts from the other DCs. The scripts folder has a few directories in it after the non-authoritative restore and those are indeed supposed to be there. However, it does not contain all of them and the ones it contains are incomplete.
I also renamed C:\Windows\ntrfs\jet and started the non-authoritative restore again in order to rule out problems related to the cache, but it also didn't lead to any success.
After restarting the non-authoritative restore, I also noticed that the scripts directory strangely did not appear in C:\Windows\SYSVOL\domain\NtFrs_PreExisting___See_EventLog, while the Policies directory did. I assumed it simply moves C:\Windows\SYSVOL\domain\ to that folder, but seems it isn't that simple. The fact that it leaves out scripts makes me wonder whether there is some database keeping track of the content in C:\Windows\SYSVOL\domain\, so that it only moves what it actually knows.
The event log does not help me much, it says SYSVOL has been initiiated successfully after the non-authoriative restore.
EDIT: For now, we got rid of this issue by reinstalling AD on the affected server. While the directory got cleared after removal, C:\Windows\Sysvol\domain\scripts remained for some reason - perhapst a problem with permissions. We then explicitly deleted C:\WINDOWS\SYSVOL and reinstalled AD again.