I'm new to Data Recovery product so i started at 1.2.
But i just came across the same limitation. I unfortunately read the admin guide for 1.0 which stated you can have more than 2 stores if they arn't used at the same time. However in the admin guide for 1.2 it states 2 stores as a limitation.
http://www.vmware.com/pdf/vdr_12_admin.pdf
Data Recovery is designed to support deduplication stores that are up to one terabyte in size and each backup
appliance is limited to using two deduplication stores. Data Recovery does not impose limits on the size of
deduplication stores, but if the size of a store exceeds one terabyte, performance may be affected. While Data
Recovery does not impose limits on deduplication store size, other factors limit deduplication shares. As a
result, deduplication stores are limited to:
- 500 GB on CIFS network shares
- 1 TB on VMDKs and RDMs