Looking over your older thread, I don't think you ever shared how exactly you installed ITFlow. I'm assuming it was manual, because the script is generally pretty good.
What database version are you on currently?
What errors do you get when you run a git pull
Have you manually edited any files?
There's no in app restore capability at the moment, so you'd need to manually backup/restore the MariaDB database. Honestly the best approach here would be to fix your current install and then do an in-place migration to a new VM. We can migrate the database as is, but it's a little more annoying as there will be schema changes that will probably hinder logging in, etc.