I have an enemy. This enemy instantiates a fireBall. I have atteched a sript to fireBall and this sript holds references for other sriptcs, but when I instantiate a prefab It will clone and references disappears, but I have added references for my script in prefab which I instantiate. I know that problem is that It has been cloned but how to get reference on scripts when I need spawn or appear a prefab in scene?][1]
You can reference the scripts upon instantiation of the clone object, or probably reference them on the fly when it needs to use them (I am guessing you are using a script to damage the player which the fireball calls, well you can use GetComponent<CharacterStat>() right there).