No, there is no simple way to fix this. Well, not without writing some fairly fancy IDE scripts (or perhaps finding some off-the-shelf script for this, though I don’t know of any off the top of my head).
I think you need to delete 199 of those gameobjects, create a prefab, and then rebuild your scene using the prefab.
Also, consider whether you really want all those prefab instances in your scene at edit time, or whether it’d be easier to instantiate them at runtime, with a bit of code in Awake or Start. Just a thought.
Or bite the bullet and make a prefab from one of your objects, delete, and start over. We all have done stuff like this. Sometimes it’s painful, and sometime it’s real painful. Try to learn from this as it’s the only positive thing that can come from screw-ups. We all seem to do these things once in a while, an unavoidable down side of being human.