For a single file:

ffmpeg -i "input.flv" -pix_fmt yuv420p -vcodec libx264 -vpre ultrafast -crf 0 "output.mp4"

If you want to encode all videos inside a folder, do this:

for i in *.flv; do ffmpeg -i "$i" -pix_fmt yuv420p -vcodec libx264 -vpre ultrafast -crf 0 "${i%.flv}.mp4"; done