Hi there,
I think that you misunderstood. In order to be able to integrate the shortcodes of the X to the Visual Composer, our development team had to change some core parts of the Visual Composer. That caused some of the original functionalities of the Visual Composer not working such as the animations. Our development team gave the option to have the original version or the modified X compatible ones.
So yes if you want to have animations you will need to use the original version and that means you will lose the ability to utilize X related shortcodes. The break you are experiencing is because of that. You already used the X related stuff.
So you either need to avoid using X related shortcodes and have the animations or avoid having the animations and use the X related stuff.
Needless to say that we strongly recommend that you use the Cornerstone for the content building as it is the official fully supported builder for the theme.
We still support the Visual Composer in regards to the updates to the Visual Composer releases but we will not implement any new feature for the builder.
Thank you.