Saving level wave settings as a prefab

So I think I've figured out an issue I had been randomly getting for months. I had saved the level wave settings in one scene as a new prefab, so there's the original prefab from you and then the one I created. This way I can use the pool boss settings in a different level and have the changes carried over. However now it automatically gives a game over even in the original scene. Every time this happens I have to completely reset up the level wave settings which can be a nightmare for my project. Have you seen this bug before or maybe know the best method of fixing it? Or do you know of an easy way to save the prefabs that I have in the pool boss so that I can just reinstall coregame kit and then paste all of those prefabs back in. Thanks for your help!