You don’t. They share the same GUID which is what is used to track that data.
There is a feature request here, Multiple Cuts Of Movie - #672 by mbarylski, that you can vote on for better handling of multiple cuts of movies. You can vote on it, but be aware the request is 8 years old, so nobody is really holding their breath on something being implemented anytime soon.
And the issue you brought up is one of multiple reasons it hasn’t been implemented yet, because that would have to be figured out since they rely on the metadata sites when they are creating that GUID.
So, basically, the answer for now (which I’m sure is not what you want to hear) is to just deal with it until Plex maybe/hopefully figures something out and implements it.
-Shark2k
