Nick here from Shopify.
I created a community topic for when things like this happen. It's called "A store with that domain name already exists" and you can see it here. It goes through all the steps you need to take to release the domain from the older store to be able to add it to the new store.
Let me know if this is what you were referring to or if it is something else, can you elaborate a little more.
All the best, Nick