I was poking around commonapp and left Columbia as my ED. However, I check today to switch ED back to Penn and start the application again, only to see that my counsellor already sent in an ED agreement to Columbia. Will this effect anything??
You can not ED to both. Penn will require the ED agreement to validate your status.
If you want to ED to Penn, you will need to switch the agreement back to Penn. You may work with customer service of Common APP and your guidance counselor to do that.