changing a bool in a prefab doesn't change in it's instance.

A prefab is only a compile-time construction. You shouldn't really mess with it at runtime without very good reason. The reason it doesn't work is that there isn't really a connection between the instances and the prefab - that's just an abstraction for the editor. Once an object is created, it's an object, not connected to the prefab, so by changing the prefab, you change only things instantiated AFTER the change.

Now, as for how to fix it, what you're looking for is a static variable. Normal variables are instance-based, that is, there's a new version of a variable for each instance. Let's try an example. Take this class definition:

 public class Test
 {
     public int a;
     public static int b;
 }

Now, if we do this:

 Test one = new Test();
 Test two = new Test();
 
 one.a = 4;
 two.a = 5;
 Test.b = 6;

We find that they each contain these values:

 one:
 a = 4
 b = 6
 
 two:
 a = 5
 b = 6

Note that the second variable is the same in both, and that we assigned it by referencing the class rather than an instance. This is because it is a static variable - it it class-based, rather than instance-based. There is only ever one copy of a static variable, and it is shared between all instances of the class. This, I think, is what you're trying to achieve, and this is a much better way to do it.