Since Hyper-V Server 2008 R2 is based on Win2K8 R2 Enterprise, that is the direction to take ... but ultimately there is no in-place upgrade.
If using VMM, then live migrate the VMs to another H-V 2K8 R2 box and flatten the existing box to do a fresh install of Win2K8 R2 Enterprise with GUI or Server Core (?).
Philip