I know this thread is old, but in case anyone searches for this, I found a way to batch convert.
Code:
for %%a in ("*.flv") do ffmpeg.exe -i "%%a" -vcodec copy -acodec copy -metadata:s:a:0 language=eng "%%~na.mp4" -map_metadata -1
pause
Open notepad, copy this text and save it with file extension .bat
Make sure both this .bat file and ffmepg.exe are in the directory of the files you wish to batch convert and drag any of the .flv files onto the .bat file icon in the folder.
This will convert all .flv files to .mp4 files and "pause" when completed.
This code also strips all the metadata from the file; like "title" "artist" etc. and sets the language tag to "English".