It sounds like the domain wasn't properly added to your hosting account.
If it were properly added, the server would treat it as an entirely separate entity, not just part of the account's primary domain.
I found https://support.godaddy.com/help/article/4688/managing-your-hosting-account-domains and https://support.godaddy.com/help/article/8342/adding-domain-names-to-your-hosting-account which might help.
Beyond that, you'll need GoDaddy's support to untangle the situation.