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Rejected tax return extension, does this mean my payment to the IRS was rejected as well?

I just received an email stating that because I had put 0 for my spouses income for a filed jointly tax extension it was rejected.  I paid my estimated tax amount during the first submission and have resubmitted a 2nd time with the corrected information. 


Can anyone tell me if the IRS will pull money owed to them from my bank account twice since I submitted the extension twice or will the IRS only remove money the 2nd extension request.  My bank account doesn have enough funds for being double charged so I need clarification ASAP.