lets say I have very long audio file, and I want to remove only right channel from BOTH (stereo) channels. Can that be done without re-encoding, just simply switching off one channel? (maybe FFMPEG??)
I don't believe this could be done without batch conversion. What you could do is load all the files into a batch converter and have them run through an effect or process that would produce the desired result, either by panning everything hard left in such a way that the right channel's content was eliminated or by panning the left channel's content to the centre and reducing the volume of the right channel to -inf. There are plug-ins that will do either.
Depending on the batch converter you use, you could replace the individual files or create copies with the channel conversion process applied.
Of course, depending on what you want these files for, you could also set the balance of a media player all the way left when you play the files or have your DAW/editor do it when you load the files into it.
I hope this helps.