TurboTax has no way of knowing that you mailed in a return with no SSN and that the dependent was denied.
Mail your amendment with the SSN and a letter explaining what happened and let the IRS sort it out.
Hold on----when did your child get the SSN? Was his SSN issued after you filed your tax return?
OH NO ... so you filed the return without a SS# for the dependent ? If so the IRS adjusted the return as they should to remove the child. Now you cannot amend the return to get any of the child tax credits allowed ... you should have waited for the SS# to be issued but there is nothing you can do about it now.
So on the original return how did you get the program to list the child as a qualified dependent ? Did you enter in a fake SS# and then erased it on the paper form ? If so you must start the amendment with the return AS CORRECTED by the IRS which means you must start the amendment process without the child listed on your return at all. Then you start the amendment process with column A of the 1040X reflecting the IRS changes to the original return. Then start the amendment process to add the child back to the return ... but be aware that the program will give you the child related credits but the IRS will once again remove most of them.