Can't remove device from icloud

Recently, Apple replaced my iphone 6s. Phone died, Geek Squad diagnosed bad logic board, they removed SIM card, gave me a loaner, sent broken phone to Apple. Find my phone was turned off online before phone was sent to Apple. Apple sends back new/refurbished phone (different serial #), put my SIM card back in it, I restored from backup and went on my way. Odd things happened: couldn't use Apple Pay anymore (won't delete card, won't add card), home security system notifications weren't working (even though I turned notifications on and off, triple checked, etc). Found that the old/broken phone is still showing up in icloud, as active/signed in, and I can't delete it. I've talked with AppleCare and they are stumped as well. Am working with a rep to fix, but no luck so far.