I ran into exactly the same problem. I had an entry in App Store Connect which was in the state of "Preparing for Submission". I was able to remove the entry from the App Store Connect. No binary was ever uploaded to the App Store at all.
When I tried to delete the AppID from the developer portal, I got the same message as @mjharper, i.e. "The App ID 'XXXXXXX' appears to be in use by the App Store, so it can not be removed at this time.".
@mjharper were you able to remove your AppID in the end?
I didn't have any ServiceID at all and I've also removed the associated provisioning profile and still no luck.
Any suggestion would be greatly appreciated.
Many thanks.