Yuck… I feel for you. I’ve been in this exact situation several times, but your desire to switch to SOs is legitimate.
In the end I bit the bullet and used it as an excuse to refactor all the little tiny things that had been bugging me before, and basically rewrote everything using ScriptableObjects.
But I did it system by system, not all-at-once. And in fact in one game I stood up a separate system alongside the Prefab-based system and kept both of them alive. Someday I might tear down the Prefabs and make equivalent SOs, but… maybe not!
ALSO: don’t even consider doing this without proper source control to guard and protect your hard-earned work.
Personally I use git (completely outside of Unity) because it is free and there are tons of tutorials out there to help you set it up as well as free places to host your repo (BitBucket, Github, Gitlab, etc.).
As far as configuring Unity to play nice with git, keep this in mind:
Here’s how I use git in one of my games, Jetpack Kurt:
Using fine-grained source control as you work to refine your engineering:
Share/Sharing source code between projects:
Setting up an appropriate .gitignore file for Unity3D:
Generally setting Unity up (includes above .gitignore concepts):
It is only simple economics that you must expend as much effort into backing it up as you feel the work is worth in the first place.
“Use source control or you will be really sad sooner or later.” - StarManta on the Unity3D forum boards