If you try to convert a MQO to a model that is not the model you originally converted, it will cause a fatal error and crash. If you have, however, kept a copy of the model (anything altered in Metasequoia will not bork it but if you add or remove or edit things in VRS it will) even without the changes that the MQO applies (ie texture or movement in Meta) then applying the MQO will work. You may have to re export the dat and switch some files names around in that case though, but that takes like 5 seconds and half a brain cell ^^
You can get some real fun stuff when you successfully apply an earlier MQO to a model that has been taken through VRS, results such as this:
(I am SOOOO lucky that I hadn't yet closed the VRS project on that one...)
But usually, it will be nice to you and close MV instead of letting you screw yourself over ^^
(it has to do with the fact that Meta does not have correct properties for altering skeletal weights for ffxi models, and the MQO file is what is altered by Meta.)