So, Update: I managed to fix the problem.

It seem at some point I had traded another egg to be raised and it was ready to be sent off to the Farm. I took the VCS Card for Amberbec to the Stables and traded it to the attendant to register as the chocobo to be my summoned mount, and she can now be used again for travel. So, Yay, problem solved~!! Hope this helps anyone else that might have had a similar situation as I did.