Hi jdonegan,
Interestingly, I had the same concern. There are a lot of valid reasons why you would want to change the variation names. This is pretty much the only thing you can't change as you can change product tile, description, images, etc. Unfortunately, support told me that if you change the attributes then the info won't sync property. I'm waiting to see if there is a work around. Ideally, the plugin should have an internal way of keeping track of attributes even if the user changes the title the customer sees on the site.