This post outlines the basic process of taking the databases offline, migrating them, mounting them in the new instance and running LCSCMD to update the pool backened.
I recently did this in a production deployment of R2 and actually found a missing step, there was also a post on the Technet forums with a user having the same issue so I figured I would post the updated process here. This may not always be the case, but a key thing to check, and what ended up being the fix in my situation was the actual pool setting in active directory.
I believe the attribute that the below command updates is msRTCSIP-BackEndServer
LCSCmd.exe /Forest /Action:UpdatePoolBackend /PoolName:<pool name> /poolbe:<SQL instance name (machineinstance name)>
When I ran through this process I found that when I opened ADSI Edit and browsed to this attribute it actually had not changed.
The DN For the pool object will be located at : CN=Poolname,CN=Pools,CN=RTC Service,CN=Microsoft,CN=System/Config Container,DC=Domain,DC=com
Again this may not always be the case but in my experience this was thef ix for the issue.