efile rejection and submission to correct issues

I just got  efile rejection due to a typo on the Federal tax ID on a pension 1099 an hour + ago.  I corrected that and then realized I needed to correct an interest payment from IRS and had overlooked 1098-T statements for both my wife and me.  I made those corrections as well and then resubmitted the efile for Fed and CA state.  The tax due amount is slightly higher for the second submission as a result.   I stupidly overwrote the existing file and pdf with the corrected tax forms (have hard copy of cover sheets and 1st 2 pages of Fed available though) when I saved everything again.  My question are

1.   "Will the electronic payment of the Fed and State taxes due be paid twice?"

2.    "Will this further confuse the IRS and CA tax folks and cause a second rejection?"