Handbrake doesn't demux like what the OP appears to want, handbrake will transcode.
Demuxing is the process of taking a file that contains both video and audio and splitting it into separate files for video, audio, etc.
Now, if the OP mis-spoke and just wants to convert the file to a different container/possibly different codec, handbrake will work.
I honestly don't know of what to use to demux a flv.
Now you can transcode the flv to something like an mkv, then use mkvtools which contains mkvextract (although you have to use the command line) and extract the audio/video/etc.