vMotion will still work as long as you have the correct EVC mode set (if needed).
I recently upgraded an environment from 4.1 to 5.5 and I created a completely new vCenter on a fresh host. I then disconnected the other hosts from the 4.1 vCenter and added them to the 5.5. I like to start fresh (especially when going from 4.1 to 5.5) if you don't need all the statistical data from the old 4.1 vCenter.
Just my .02