А как насчет этого:
readarray -t arr < file
counter=1
for i in "${arr[@]}"; do
for k in "${!arr[@]}"; do
if [[ ! -z "${arr[$k+$counter]}" ]]; then
f1="${i}"
f2="${arr[$k+$counter]}"
ffmpeg -hide_banner -nostats -i "${f1}" -i "${f2}" -filter_complex signature=detectmode=full:nb_inputs=2 -f null - < /dev/null
else
break
fi
done
(( counter++ ))
done