First, see slhck's blog post on superuser for a good FFmpeg tutorial. FLV is a container format and can support several different video formats such as H.264 and audio formats such as AAC and MP3. The MP4 container can also support H.264 and AAC, so if your input uses these formats then you can simply "copy and paste" the video and audio from the mp4 to the flv. This will preserve the quality because there is no re-encoding. These two examples do the same thing, which is copying video and audio from the mp4 to the flv, but the ffmpeg syntax varies depending on your ffmpeg version. If one doesn't work then try the other:
ffmpeg -i input.mp4 -c copy output.flv
ffmpeg -i input.mp4 -vcodec copy -acodec copy output.flv
However, you did not supply any information about your input, so these examples may not work for you. To reduce the file size you will need to re-encode. The link I provided shows how to do that. Pay special attention to the Constant Rate Factor section.
ffmpeg.exe -y -timelimit 60 -xerror -i mega.mp4 -qmin 2 -qmax 8 -ar 44100 mega2.flv
Or just :ffmpeg.exe mega.mp4 mega.flv
whitout a good result. – John_D