Use the following command to convert FLV file to MP4.
ffmpeg -i source.flv output.mp4
If you received error (Codec is experimental but experimental codecs are not enabled, try -strict -2) when trying to use the command above, you can try
ffmpeg -i source.flv -strict -2 output.mp4
If you would like to change the bit rate, you can add in ar option.
ffmpeg -i source.flv -ar 22050 output.mp4