Do I need to file on paper when my son first failed to check that he can be claimed as a dependent but now has amended his return which has been complete and adjusted?

I am receiving a rejected return when I attempt to e-file. It states that a dependent SSN on my return must not be that same as another return with the dependent box not checked. I filed an extension to wait until his amended return went through and was complete. I still get a rejected return even after receiving notice that his return has been amended. He first filed electronically and then had to amend by paper.