SYSVOL/NETLOGON Replication problems in domain

This problem is so complex, I'll just stick to the basic...

I manage a child domain, in which it's divided in 4 sites in AD.  Each site has 2 DCs under this child domain.    I noticed when applying a change in GP, not all the sites were being affected by the change.  I found out that the actual GPO folder in SYSVOL wasn't being updated in the problematic sites.   I forced replications (via Sites and Services) to no avail.  I manually copied the updated GPO folders in each Sysvol folders in each DC.  (which "fixed" that particular GP issue)

I then tested Netlogon.  In each site, i created a text file in one DC  in each site naming it "a_[site_name].txt" (i therefore created 4 different text files in  the Netlogon folder)  I found that the text files weren't all replicated everywhere (with the exception of one site, which had all 4 text files).  

What I found to be interesting is that the Global Catalog DC did not contain any of the 4 text files (in the site where the GC is at, I created the text file in a 'secondary' DC).  

I did dabble a bit in creating manual connections in Sites and Services, but didn't want to go to far.  I'd hate to have that 'resolve' this since I'm sure there's a more underlying problem than "site A doesn't replicate to site B".

Environment:  Windows Server 2008 R2

I know I'm missing something but this is a start.  So, help is appreciated, as always.  
Thank you.
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Sarang TinguriaConnect With a Mentor Sr EngineerCommented:
first check that you have proper Connection objects has been created in Sites and Services
Run repadmin /replsum to check that your replication is good

Browse \\WorkingDC.domain.local copy sysvol & netlogon and keep backup on ProblemDC &  WorkingDC (If can not browse check network connectivity/Port and don't proceed further)

Go to WorkingDC  stop NTFRS service open regedit and go to "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\NtFrs\Parameters\Backup/Restore\Process at Startup" change the burflag value to D4 Start NTFRS(File Replication service) service and wait for File Replication event ID 13516 now Go to ProblemDC  stop NTFRS service open regedit go to "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\NtFrs\Parameters\Backup/Restore\Process at Startup" change the burflag value to D2 -> Start NTFRS(File Replication service) service and wait for File Replication event ID 13516 now

Check Now your sysvol and netlogon shares are available

Above is called Authoritive(D4) and non-Authoritive Restore (D2)

Refer for more info
Sarang TinguriaSr EngineerCommented:
Are you using FRS or DFS for sysvol replication..
Did you look into the DFS log file?
Are there any errors?
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OrmatAuthor Commented:
your comments pose an interesting question - how can i tell if i'm using either frs of dfs for replications?
You can follow the quite similar discussion in EE also

Also you can follow the technet support also
OrmatAuthor Commented:
wow. ran a burflag (d2) since i saw journal wrap errors on a dc, and now the netlogon is missing.. rather, all the shares. now what?!? :)   am i supposed to remove "d2" after having restarted the fsr service?
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