I suggest keeping the files for each movie in their own folders, if you don’t already do so. The filenames are also very important. Here’s a screenshot of my files for the same two movies (I’m also on linux). The highlighted parts of the filenames are the most important – the imdb numbers could help, though.
If you rename/reorganize the files, you should probably do the Plex Dance afterward.
There may be other ways to go about this, but Plex has never tried to merge these two movies into one on my server.
