Please update to the latest service pack before migrating SYSVOL from FRS to DFSR on Windows Server 2008. Migrations on Windows Server 2008 SP1 may fail due to downstream servers trying to replicate the same file(s) from their upstream partners that no longer exist.
This issue is resolved in Windows Server 2008 SP2 and also in Windows Server 2008 R2. If you have already begun your migration and suspect you have encountered this problem please contact Microsoft Support. If you have started your migration and encounter this issue, upgrading to the latest service pack will not resolve the issue. You will need to contact Microsoft Support.
To encounter this problem the non-primary member that is stuck in initial replication must be replicating from a DC that was not the original primary member. Normally the PDC emulator is the primary member for SYSVOL migrations. DFSR replication for SYSVOL migrations follows the AD replication topology. If you have more than one AD site defined it is possible you may encounter this issue during SYSVOL migration.
DC1 and DC2 are in Site A
DC3 and DC4 are in Site B
DC1 is the PDC emulator and the bridgehead server for site A. DC3 is the bridgehead server for Site B.
Note: As DFSR replication for a SYSVOL migration uses the AD replication topology DC1 will replicate with only DC3 in Site B as they are the bridgehead servers for their respective sites.
SYSVOL migration begins
DC1 is the primary member for the SYSVOL and successfully replicates with DC2 and DC3
DC3 incorrectly leaves some unique entries in its DB when it moves unique files to the pre-existing directory
DC4 begins initial replication and uses DC3 as its source
DC4 is stuck in initial replication trying to replicate the files DC3 left in its DB in step 3