I had a shell wrapper script to convert MTS files with FFmpeg, but somehow, when running on multiple files, only the very first one got converted.

Turns out that FFmpeg swallows the stdin from the bash script when it is run and therefore nothing remains in the stdin for the next iterations. To remedy this, I had to fake input to ffmpeg:

while read movie
do
echo "" | ffmpeg -i "$movie" -vcodec copy -acodec copy "$movie".mov
done

Without the echo command this would’ve ended after first iteration, regardless of the number of files in the input.

BTW, the above command is useful for turning MTS files into MOV files, while preserving the audio-video streams, for software that does not support MTS.