Executing code on prefabs that are never instaciated + data loss

I have been using this interesting approach of having prefabs that reside in the project. Each prefab has a script that contains behavior and references a scriptable object which contains the defined behavior (like a preset). Recently I have noticed the prefabs data being corrupted, the prefabs loosing reference to their scriptable object properties and other unwanted behavior.

I am assuming that these problem stem from the prefab running code (instead of an instance doing that) and thus modifying the prefab instead of an instance. Now I want to continue keeping the definition of this behavior outside of the scene.

If you have made experiences with this sort of behavior or have any ideas how I can keep my system procedural without having to instanciate a bunch of stuff that would be neat. I was thinking of moving the logic to scriptable objects as well although that would be a bit of a compromise and I am not sure if that makes sense at all...