Rejected 1040 being used to calculate amended amounts on 1040X

My original e-filed return was rejected by the IRS because my dependent had already been claimed. I removed him as my dependent, re-filed and it was accepted (with my new EITC and child tax credit adjusted to reflect him being removed). My other non-dependent child was used to calculate my EITC (even though I stated that her other parent was claiming her) so when he tried to file, his was rejected because her SSN had already been used to file an EITC (mine). I waited for TurboTax to release the amendment software, and began filing a 1040X amended return to remove her from my EITC. TurboTax is using the original 1040 that was rejected by the IRS for having my son claimed. So when it calculates what is due for removing the EITC for my daughter, it is also calculating removing him and creating a 1040X that shows I owe his child tax credit, the EITC for him, and the EITC for my daughter. How do I get TurboTax to use the accepted 1040 to calculate what I owe?