try to include a number… I don’t think the file format matters in this:
Stargate SG-1 - s08e18 - Threads.m4v
Stargate SG-1 - s08e18 - Threads-deleted1.m4v
Stargate SG-1 - s08e18 - Threads-deleted2.mkv
I remember drzoidberg mentioned that’s currently the only way to have multiple extras of the same type on episode level. Personally I’m still hoping for some refinement to allow us some kind of subfolder handling for the episode level local extras; e.g.
Stargate SG-1 - s08e18 - Threads.m4v
Stargate SG-1 - s08e18 - Threads-deleted
Deleted Scene 1.m4v
Deleted Scene 2.mkv
OR
Stargate SG-1 - s08e18 - Threads.m4v
Stargate SG-1 - s08e18-deleted
Deleted Scene 1.m4v
Deleted Scene 2.mkv
OR
Stargate SG-1 - s08e18 - Threads
Stargate SG-1 - s08e18 - Threads.m4v
Deleted Scenes
Deleted Scene 1.m4v
Deleted Scene 2.mkv
just some random rambling 
Edit:
I’d love to be able to include named deleted scenes for some episodes (where those extras had their own names on their source discs)