The ConfigMgr team recently published a blog post on the supported use of Data DeDuplication with ConfigMgr 2012 R2. Here is a Geek's summary of the 1500 word blog post:
1. Data DeDuplication is awesome!
2. ConfigMgr 2012 R2 supports Data DeDuplication on the following ConfigMgr folders only:
- Content Library (SCCMContentLib)
Note #1: This means you cannot have your source locations in a Data Deduplication scenario, only the above folders.
Note #2: Since Data DeDuplication is enabled on a per volume basis, you need to exclude any other ConfigMgr folders you may have on that volume.
PowerShell is King
Fellow deployment geek, David O'Brien, has written has nice post on configuring DeDup for ConfigMgr using PowerShell: https://david-obrien.net/2014/02/enable-deduplication-powershell-configmgr-exclusions/