Plex supports having multiple source files for the same movie/episode. So, storing the “optimized” version as a copy and just letting me select which version to play might be an option. Same when deleting the content, Plex already gives an option to delete, and if more than one version of a movie exists, it asks which one to delete. So a user can optimize and then choose which version to keep. Such an option would significantly lower the barrier, letting less experienced people maintain the server and reducing the hassle, providing a reliable workaround to those struggling with unsupported media, too many streams, too slow network, etc.
And probably will also be a solution for people asking for this feature [Feature Request] Keep the optimized movie version only - #17 by scarecrow365