Select one or more objects, go to the "GameObject->Replace selected" menu. Assign the object/prefab they should be replaced with and hit "Replace selected". You can undo this operation via CTRL+Z.
The "Keep prefab overrides" option will apply any overrides to the newly replaced object. This only works if the original object was also a prefab.
Note: objects that are part of a prefab instance cannot be replaced, since prefabs may not be directly modified.