The app was originally created under a developer's appleID and the published in the Business To Business site. The developer left the company and the company created an appleID to be used for the company's development purposes. (Which is what should have been done to begin with).
The app was then transferred to the company's ID however the transfer didn't work right as it left the AppID under the old developer account so any attempt to use certificates and profiles against either account was doomed to failure while using the original AppID. To do any sort of internal deployment, a different AppID had to be created.
After Apple finally got the app transfer fully complete, all was good and the original AppID could once again be used.