If you are on a MAC and if you have a copy of Adobe After Effects, you might try looking into Dashwood Stereo 3D Toolbox – https://www.dashwood3d.com/stereo3dtoolbox.php
The plugin allows you to isolate a side by side input to either the left and or the right eye only. That way, you can isolate each eye and export a master file separately.
If you are on Windows, well I am not sure if this would work but I suggest you look into Vegas software – which has built in stereo filters.
The current STEREO workflow for Adobe Premiere Pro CS5.5 relies on a plugin called Cineform. I have a working Neo 3D license and I think there’s no way to isolate either the left and right if the file has not been muxed or created inside CIneform itself.