Adding/removing vMotion capabilities will not mess up VCD VM's like enable/disable DRS does. It will just allow VM's to live migrate from one host to the other.
Some times I forget to enable it on my new hosts and don't realize it until I try to vMotion VM's to it. At that point I have already prepared the host within VCD. I then setup vMotion and it starts working without putting the host in Maintenance Mode to do the work.
-Eric