PMS 1.26.1.5772, using Plex Movie scanner & agent.
Each version in separate folders:
.../test-movies/Its a Wonderful Life (1946) [bw]/Its a Wonderful Life (1946) [bw].mkv
.../test-movies/Its a Wonderful Life (1946) [color]/Its a Wonderful Life (1946) [color].mkv
Add both to the server, Plex combines them as duplicates:

Split them apart:

Result after split, two movies with same name:

Edit one of the movies (pencil icon, lower left corner), look at Info tab to determine version:
Go to General tab, edit Title to reflect version, Save Changes:
Repeat for color version.
Result after changing both movies:


