@enmus I’ve attempted to rewrite the title to be more explicit about the issue. But let me know if I totally butchered it and just change it back.
Let me say that I totally understand your reasoning for this. Actually, I did exactly what you suggested in your first post. When moving to 4.1 I didn’t restore the default templates.
Instead, I opted to reinstall all the software I had there. To do this I used commands like dnf history (on fedora templates) to see what else I had installed. There should be a similar one for debian.
Then I also looked at the file .bash_history to see the commands I had run on the template to recall any other changes. Since they are templates, I didn’t to a lot there so it was relatively simple.
In the future (and this is advanced stuff), you can take a look at saltstack. It’s a way for you to setup Qubes just the way you want it in a predictable way. In case you’re not familiar, think of it as a recipe for what qubes, packages and configurations you want. Then all you have to do is run it (even on a new system) and it sets everything up for you. (this is what Qubes uses internally to setup the whole system).