After you file

Of course TT has the 1040X ... you even mentioned the 1040X was not allowed because they were updating the program and the IRS requested that it be taken offline for a while to keep folks from doing exactly what you did.  The "superseded" return will most likely be ignored but time will tell.   And the return you MAILED in will take months to even see the light of day ... there was no possible way for it to possibly stop the original return in the processing que.