If you have Hyper-V running on your 2008 server, your upgrade to R2 is going to be a little different. Here’s some information on upgrading the two main types.
Upgrading a single host
The steps to upgrade a single Windows Server 2008 or Windows Server 2008 Hyper-V RTM host are outlined in Microsoft Knowledgebase Article 957256. Both an in-place upgrade and transition scenario is available.
Although the in-place upgrade method reports the Hyper-V role needs to be uninstalled before upgrading, the only actions required are:
Transitioning from a Windows Server 2008 Hyper-V host to a Windows Server 2008 R2 Hyper-V host is a matter of exporting and importing your virtual machines. Of course, to export a virtual machines means to shut it down. Snapshots need to be merged before exporting and after you import the virtual machine, updating the Integration Services is necessary. Alternatively you can use your favorite backup program to backup your virtual machines on your Windows Server 2008 Hyper-V host and restore them to your Windows Server 2008 R2 Hyper-V host. Donâ€™t forget to install the Integration Services afterwardsâ€¦
Upgrading a cluster
Another story applies to Windows Server 2008 clusters. Since rolling upgrades to a failover cluster running Windows Server 2008 R2 are not possible, youâ€™re stuck with using the Cluster migration wizard. You can use the wizard to migrate to a brand spanking new cluster on new hardware or migrate to a new cluster, created by performing a two-step eviction of your Windows Server 2008 Hyper-V cluster to add the nodes individually to a new Windows Server 2008 R2 Hyper-V cluster.
The â€œMigrating Settings to a Failover Cluster Running Windows Server 2008 R2â€ Windows TechCenter article explains both migration scenarioâ€™s in depth.