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Cleaning up FRS Sysvol Morphed Folders without Rename

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Hello All
I am Mahesh
Currently I am in process of migrating FRS Sysvol to DFSR Sysvol. However I have one problem.
I have so many morphed folders (some are empty) underneath Sysvol\Policies\GPO_Guid\_NTFRSxxxxxxxx
I got MS article http://support.microsoft.com/kb/328492 to remove Morphed folders.
Since My environment has more than 100 2008 R2 domain controllers, I don't want to follow above article as It involves some downtime during clean-up.
Let me know if I can just delete those Morphed folders from Sysvol ? OR
let me know if I can directly go for SYSVOL FRS to DFSR Migration and Can DFSR take care of Morphed folders
Request your expert advice please.
Thanks in advance
Mahesh
mahesh1000@gmail.com

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