Based upon the documentation, I run the hcirootcopy to completion. Then take down the engine under the old version, then bring it up under the new version. However, I have some files that our engine writes to while running and if they get copied prior to bringing the engine down, it will not get the latest version of the file(s).
It appears that to be safe, I should bring the engine down prior to running the hcirootcopy.