Ok, I'm somewhat unclear on what exactly the situation is.
Let's call the host you upgraded from 5.1 to 5.5 Host A and the host that was already upgraded to 5.5 Host B.
1. You migrated the VM's and the VR appliance from Host A to Host B.
2. You upgraded Host A from 5.1 to 5.5
3. You migrated some of the VM's (but no the VR server?) from Host B back to Host A.
4. The VM's back on Host A work but the ones on Host B don't work?
5. If you migrate the other VM's back to Host A they work, but migrating the VM's to any host besides host A doesn't work.
Is that right?
Double check that your upgraded setup still allows network traffic to flow from the affected servers to the VR server.
Did you have replication set to go out to a particular vmknic under 5.1?