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Sysvol cleanup

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I have inherited a AD environment that is in much need of some TLC.  Using the script found on:

https://social.technet.microsoft.com/wiki/contents/articles/52209.active-directory-find-and-treat-orphaned-group-policy-objects.aspx

My environment is showing that it has 25 phantom items.

24 of which are listed under a GUID and 1 is a PolicyDefinitions

I am looking for info on how to clean this up as safely as possible and exactly what steps i should take to backup and how to recover.

Little bit more background, when i first started going through the environment i found about a dozen GPO's that had revision mismatches via the below link and was able to get them all in sync by making a small change on the affected GPO's and then reverting the change.  Right now i am running this script daily and manually watching just to make sure nothing goes out of wack again.  Future plans is to try to figure out a way to automate this and roll it into a monitoring solution. 

https://gallery.technet.microsoft.com/Get-GPO-Replication-4db47c83

My other future plans are to check for any Disabled / unlinked GPO's and to find out why they are still there and try to remove them as well. 

Any help / suggestions on the initial cleanup of the phantom objects or other ideas for cleanup and what to check for would be appreciated.  Just a note on top of this, the current environment is still only a 2008 R2 functional level and has not made the migration to DFRS for sysvol replication.  I figure i want to get this as cleaned up as possible before I make any more moves, but with 2008R2 going EoL by end of year i need to move somewhat fast.


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