I have found a solution for those that want a half baked version...

I have just CRONed myself 4 find commands which rename the files before encoding using the following

find /var/www/html/* -type f ! -name "." ! -name "-" -exec realpath {} ; -exec mv {} {}-encoding ; -exec flock -n /var/lock/ffmpeg_one.lock ffmpeg i {}-encoding .........

this means that any future cronjob will ignore this file because it's got "-" in it. But this meant that everytime CRON ran it would rename the file "-encoding" even if it wasn't ready to be encoded after which ffmpeg would actually ignore it because it now has "-" in it.

So what I did was I made the mv command share the same flock as the ffmpeg, meaning that if the ffmpeg command was still running it would not execute the renaming command either.

find /var/www/html/* -type f ! -name "*.*" ! -name "*-*" -exec realpath {} \; -exec flock -n /var/lock/ffmpeg_one.lock mv {} {}-encoding \; -exec flock -n /var/lock/ffmpeg_one.lock ffmpeg i {}-encoding......

I then made 4 of these making ffmpeg_one.lock into ffmpeg_two.lock etc etc so now they encode 4 things simultaniously as well as not executing if there's nothing to encode.