If you need to re-encode a lot of videos all at once, each video being in a different folder, here is a little bash script for you. Just put everything in a file and execute it. The file needs to be executed in the main directory where all the children folders are. If you have spaces in the name of the files, it’ll still work.
#!/bin/bash
for folder in "*"/
do
for file in "$folder"/"*".flv
do
ffmpeg -i $file ${file%.*}.mp4
done
done
It’s easy to understand, so you can adapt it to your own needs easily.