Not serializable anymore when also a prefab

Hi, I've been working with Custom Editors and Serializable classes for a while now and I've noticed something that might pose a problem for me. I've seen that once a prefab has been made of an object, the object in the scene itself isn't serializable anymore. All changes made to the instance of the object are reverted once you execute the game. It's only editable via the inspector of the prefab. However if there's no prefab of the object, it's still editable via the scene.

Does anyone know how to work around this? So that the instance can still be edited without altering the prefab?