So I’ve been having this mystery problem with Server 2012 R2 for a while now. I have a 2TB external drive that I am using for backup storage. I was running out of space on the drive, and I couldn’t figure out why. When I added up the files on the drive, they didn’t come anywhere near 2TB. In fact, I moved everything off of the drive entirely and I still had only 32 GB free! Something was definitely awry, and I had to figure out what.

My first thought was to just re-initialize the drive and go on with my life, but then I would always be left wondering what caused it. So instead I investigated until I found the problem, and hopefully this article will help someone else resolve the issue without having to shuffle tons of data around to re-initialize a drive.

First some background information: I went through an experimental phase with data deduplication. I found that it worked wonders on my standard data drive, but it did zip shit for my drive that was storing local backups. That is because the backup software I use (CrashPlan) already does data deduplication. So I disabled it on the backup volume and left it running on the data volume. Great, right? Almost.

There was some cleanup that should have happened but didn’t. Namely, the Dedup folder that sits just out of reach under the System Volume Information folder. Even if you adjust the security settings and ownership of the System Volume Information folder, Windows won’t let you touch it. It thinks that it’s smarter than you! Well… I proved otherwise.

*** DISCLAIMER *** I offer the following information with no warranty whatsoever. This is for information purposes only, and should you royally wreck your system by attempting to follow these instructions, it’s your own damned fault. Play with the System Volume Information folder at your own peril.

So how do we clean that up without unmounting the volume or re-initializing it? Simple… we attack it from another machine. First, go into the advanced security settings for the System Volume Information folder in question. I’m not going to go into detail about the steps involved. If you don’t know how to do that, then you probably shouldn’t be poking around in there to begin with. Next, change ownership of the folder to the local administrators group and give the local administrators group full access. Check both the “replace owner on subcontainers and objects” and the “replace all child object permissions…” check boxes. Even though this will complete, Server 2012 still won’t let you access it directly.

You have to be sneaky and hop on another workstation. Use the administrative share for the drive to access it. Open up Windows Explorer and use the UNC path (change to suit your situation of course): \\server1.yourdomain.com\e$\System Volume Information. Once you have successfully gained access to the System Volume Information, you can root out and delete the offending files that should have been cleaned up.

Be careful, because you can wreck things pretty bad if you don’t know what you’re doing in there. For my case, what I needed to do was remove the Dedup folder. This was taking up 1.7 TB of space, and I had deduplication disabled on that volume. Interestingly enough, when I used the CLI commands for administering deduplication, it showed metadata for the drive in question before I surgically removed the junk files. After I removed the Dedup folder from the System Volume Information folder, the CLI commands no longer displayed any dedup info for that vollume.

Oh… and I got all my drive space back! I hope this helps someone who’s gone and made a fine mess of their system as I had.