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Suppose you have a prefab Spawner that has a variable frequency and a link to a GameObject SpawnZone.
You instantiate Spawner in your scene, attach a SpawnZone (an object local to scene), and play with the frequency. When you have it the way you like it, you apply the changes to the prefab.
Of course, the prefab will now get your updated frequency and won't get your SpawnZone.
The surprise: Unity also silently rips the link to your SpawnZone out of your local instantiation of Spawner. You have to manually reattach it.
