When I add prefabs to the scene, the instances lose their connection to the original prefabs in play mode.

Before play mode:

In Play mode:

If I instantiate them during runtime with PrefabUtility.InstantiatePrefab(prefab) instead,
the instances keep their connection to the original prefab.

Problem

Since the instances lose their connection to the original prefab, PrefabUtility.RevertObjectOverride can’t be used to reset them to their original state.

Question

Is there a way to add prefabs to the scene while keeping their connection to the original prefab during play mode?
Is there a different (maybe even better) way to reset the prefab instances to their original state?