paris_wendy,
if you are looking for an alternative for Prinergy that is compatible with nexus: there used to be software from artwork systems that kept track of all your files, but I can't recall it's name. Maybe there is someting from esko that can help you with that now.
Your backup solution sounds good allready, but maybe you should consider changing your workflows so that nexus does the job for your operator. If nexus can connect to that computer then you just need to add a few activities. First you need a select file that selects all of your files from the job folder and then a copy ftp to your destination (if I'm not mistaken).
I hope this works out, 'cause it'll save you and your colleages alot of work and error-free backups of the files.