And his original certificate would still be there, that is never changed.
When a child is adopted, the original is sealed. It cannot be released without a court order. Neither the State nor the Federal government wants individuals to possess two different birth certificates which can be used for identification purposes.
Obama's legal team may have requested the production of a new birth certificate rather than an unsealing of the original. I think the only person that could answer this question authoritatively is a lawyer or judge who has been involved in a similar process.