Renamed Instances won't work. No way around it for now.
Per Follow Liker Help Desk, you can rename Instances, but when you try to load them back, they won't work. There are many files associated with an instance. So even if you change all those other files, the Instance just doesn't work.
The only thing you can do is make new Instances with the name you want. And, go back and delete the old ones that you don't want.
It sucks, but I hope FL can let us rename Instances in a future update.