If you only want to convert, for example, MKV to MP4 then you will save quality and a lot of time by just changing the containers. Both of these are just wrappers over the same content so the CPU only needs to do a little work. Don’t re encode as you will definitely lose quality. Open a terminal and write:
for i in *.mkv; do
ffmpeg -i "$i" -codec copy "${i%.*}.mp4"
done