I'm not sure either.  I efiled a superseding return last week two days after the original return (same deal, lower refund on second filing).  I expect the client will get the full original refund and then have to repay the excess.  What I told my client "In a perfect world the IRS computer would know that there was a superseding return on file before releasing the refund from the original return. But unfortunately we live in this world instead. :("