For some of my movies I have both an 1080p and a 4k Version saved into the same folder. Emby groups the files together properly and allows me to pick the version I want to watch.
It seems that there are a few movies that just refuse to be added into a Collection when I do this.
My John Wick movies show in a collection and have both 4K and HD in the same file. As will my Pacific Rim Movies.
My Matrix Movies, will not go into a collection (even if I try to add them manually), The Incredibles will also not allow me to add them to a collection.
I use the same file name structure for all of my movies.