Hey!
Thanks for the reply, global variables ended up being the way to tackle it.
Still migrating some things over to it, and my animation FSM is behaving strangely, but I'll figure that out.
I just added a simple FSM to each object I needed to refer to that saves itself as a global variable when the level starts, then just referred to that global rather than the object itself, as I was doing prior to migrating everything to prefabs.