That sounds like a lot of work to me! To be honest. Wow. I have a fully automated system here. I rarely have to do anything regarding new class creations and backups and tons of other stuff, like attendance. We have Registrar staffing that takes care of classroom assignments with our entire student body. We have a student management system, hybridized from a commercial product and things I've added in to accommodate our needs with a web interface I made also. That system is what they use exclusively. The programs I wrote to bridge Moodle with the backend system were a bit of programming, sure, but that time has paid for itself so many times over. Without those programs and custom software they would need to hire two more people. And on top of that, I'm free to use my creative skills in other areas for the college that they didn't hire me for, which is what I've been doing for years.
I also made a "Web Lab Server" for our Web Design program. Students in that program have their own webspace, with PHP, MySql, ASP.net 4.5 support. Each one gets their own webspace with their own path. And that system is automated too now. New enrollees are automatically created in the Web Lab system. This allows them to have a public place on the internet to show off their work, and/or utilize for classroom work, homework, etc.
Anyway, there'd be no reason to go back to a system of scripts that require a human being to execute many times over, changing file names, copying files, etc. However, coming from a place of nothing and doing everything manually otherwise, your approach makes logical sense.
Thanks for your input along the way. I'm very pleased I found the cure. To be honest I was doubting if Moodle was still using the same Backup 2.0 object methods. Glad to know it was a database issue. Now, on to discover how those tables went missing...