This tool can help you to replce new Game Object with old Game Object in Unity
its work with local tranform and instantiate prefab insted cloning (normal instantiate)
options:
1. replacing one newObject with one oldObject
2. replacing one newObject with oldObject childern
3. replacing one newObject with a list of oldObjects
you can easly go on Tools->InstantiateObjects or just press CTRL+F1
Update V0.2
for masive number of gameObjects now you can just select them and click on "+" button to add them easily.
Update V0.3
add a button to clear old gameObject list