Update on this one.

It's just happened again. This time I know that it was firewall related. The firewall settings were changed and, for a couple of hours, the FTP Server was not reachable by FME Server. After a couple of hours, once the firewall settings were back in place, FME Server Re detected all the files on the server as 'newly created' Triggering all the jobs to run again.

Perhaps @jlutherthomas you could help me understand how this might have happened and how I might be able to prevent it in case it happens again.