I accidentally filed EIC and now my son's father's return has been rejected.

I know that I must wait for my refund to be deposited in my account.  I then plan on mailing an amendment form along with a check for what I owe back to the IRS.  I understand this takes a few months to be processed.  In the meantime, the father plans on mailing his return in.  I understand that he will get his refund.  Will there still be an audit if my amendment is still in the processing stage?  Should he file an extension and wait for my amendment to be completely processed (16 weeks)?