When one backs up a course, one has options ... step through that once and you'll see it looks inclusive .. i,e all users, all grades, all assignments turned in, etc. IF the same students are to be in the course after restored. IF not, one could make a backup with 'no users' ... no turned in assignments are included in the backups as those are tied to users. Restore of that course should be like re-setting a course (resources etc. stay, but student data and students are removed).
However, having said that, that's the way it's supposed to work.
To comment upon using Softaculous for upgrades ... a poster did say it worked. Suggest conversing with the person directly.
Adding to what Howard mentioned, you've turned over installation/upgrading to them. If their software doesn't install or upgrade successfully in EVERY instance, then, IMHO, one should be contacting Soft... first. I've had no issues upgrading the command line way.
Seems they do what's easiest for them ... tell you to come to these forums with the problems. Hope you don't pay for that! Hmmmm ... wonder how many users in these forums actually use your hosting provider, your plan, that version of Soft... etc..
Anyway ... that's my 2 cent advice! ;)
'spirit of sharing', Ken