Prefab works when created, stops working when unity is closed and reopened.

This is a weird one. One of the devs at our company called it “schizophrenic.” So, we have this prefab in one project that represents a breaker switch power supply combo. We send messages to a solver via java and it tells the power switch if it can go up or down. Super simple right? Works perfectly. We have a virtually identical second project (the scene has different stuff in it but retains the same hierarchy and folder structure. We drag the prefab of the breaker over to the second project and run it, again, it works perfectly. Then, if I change the scene or close unity or commit to the repo it borks. It only sends an off message ever after. The power switch no longer moves. We are all banging our heads against the wall and we are suppose to have this ready for production yesterday. Does anyone have a clue what this is? Some of us are very experienced and we still can not solve it. I myself have tried everything I can think of but no matter what it keeps happening. One thing to note, if the prefab is in the second project folders, it still works if we drag another copy. That copy in the scene malfunctions again and again and again if we repeat the bork process of closing unity or changing scenes. Any help would be massively appreciated. I don’t know if this breaks any rules but I would offer an award. We can’t test without a power supply lol. We are using unity version 2020.1.6f1. I can answer any questions anyone needs. Code samples etc. We don’t think it is our code we think it’s unity magic somewhere. Can anyone help us?

This is the sob right here.

Have you tried a clean minimal project and import just this prefab from an exported Assets package?
Isolate it to the maximum and scatter tests and Debug.Log() all around. Somewhere you should get a null message or other error. Good luck.