I don't think it's as much comprehensive skills as much as it's fear. Fear that something might go wrong and then they've lost data, a computer and a noticeable amount of finances out of a lot of assumed tight budgets to begin with. I'm learning stuff on my own but it still doesn't take away the fear that I might fuck something up and then pay a couple hundred dollars to undo it. Not like I have a potato to practice on and I'm sure others are in that same boat.
even it's off-topic, but if you fear to break something by trying to refactor a simple RenPy game, then you're right - better don't touch it, because you seem to lack even the bare basics. It's impossible to damage something by refactoring a RenPy game. The most you can damage are your origin data files and lose them (if you didn't backup them before starting to work with them).
To damage any hardware shouldn't be possible at all. At most you could damage some files. And even if, there's always your system backup.
General rule: No backup? No mercy!
If you wanna try, and still have fears, here's a pro-tip:
Nowadays no one should run the system on bare metal (meaning operating system directly installed on hardware).
You should run a virtual machine (for example Microsoft HyperV - not the best, but free to use if you got a Windows professional Edition - it's a standard module of Windows professional installation media, but deactivated and not being installed by default). Inside the VM you install your Windows as usual - the VM will work same as your PC. Basically when you start your PC, the VM will start first, then you start your virtual PC with Windows on it (or any other OS of your choice) inside this VM. You can also have multile VMs with different OS running if you want to.
Benefit of that, you can do simple snapshots of your VIRTUAL system at any time, and once something is broken (or even if you got infected by malicious software), simply stop the Virtual Machine and restart it again with last snapshot and everything is smooth again. This also protects you 100% from remote hacking, as the hacker will be inside your VM and you can always stop the VM and restart it again from last snapshot like nothing happened at all).
TL/DR:
It's neither impossible to refactor the game, nor is there barely any risk to damage something (100% none, if you take basic precautions, which i would recommend to do anyways regardless this topic of breaking something).
It's more a matter of effort and time to invest to refactor the game into one big game - compared to the benefit on success. Why not simply play all parts one after each other? It's just not worth the effort to invest - simple as that