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Its a different type of extension - its an automatic extension for two months but requires a statement attached to your return.  I am not sure if you are able to bypass that one and proceed with a regular extension filing.  My hope was that this method would lead you back into your actual extension filing and you could resubmit.  It appears that isn't the case and I would assume that it would get marked as a new filing and not "fixing your rejected" one.  You might want to check back tomorrow and if others are having this issue, there may be more information available for a fix or workaround by that time.  Otherwise, it might be easiest at this point to mail the extension.  You can include a copy of the rejection confirmation (but the IRS will have it in their system).