Server Is Not Functional After Uninstalling Commerce Server
Commerce Server 2009 R2 and Microsoft BizTalk Server share some functionality related to the Profiles System. If you have both Commerce Server 2009 R2 and BizTalk Server installed on the same computer, and you uninstall one of them, some functionality in the other product may be compromised.
To resolve this issue, use the Repair mode in Commerce Server 2009 R2 setup or BizTalk Server setup to reinstall any components that were accidentally removed when you uninstalled the other product.