No - go ahead and e-file the return. The IRS has a record of your extension.
The ONLY way to accomplish e-filing a copy of the 7004 is to include it in the same PDF file as the 8453, the signature form.
The program is designed to upload and attach a file containing an 8453-S that is required for efiling. The additional attachment that you want to efile can be combined into the same PDF (or image file) as the 8453-S and then uploaded and attached to your return. That entire file should be transmitted along with the rest of the forms in your return.
Again there are no guarantees, but that is the only way to attach and efile any kind of form in the program.
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