
Maybe try:
If each user does have a home folder. Then make sure to create the project there and then save all and all files will be written there.
Work with your sysadmins/IT . There's probably a way forward.
When you install OpenToonz you can choose where to put the "OpenToonz 1.0 stuff" folder. You could install that folder onto a network drive or someplace that doesn't get wiped perhaps.
I think this is incredibly cool that you're doing this for your students and I have no doubt in my mind that you'll greatly inspire them. I wish that my school had something like this when I was studying back in the day :). Best of luck to you and your hard workers! Are you going to be posting the "Alien Wars" final short anywhere online for the public? Let us know =).
As a possible solution to the saving location- I am working on a portable version of OpenToonz that will run from any folder without installing.
I have it working already, but just need to make sure there aren't any bugs.