This is from the Internal Revenue Manual:
21.5.3.1 (09-07-2017)
Program Scope and Objectives
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Purpose: This IRM contains the guidelines for identifying claims and the processing steps necessary to complete the case, along with the required taxpayer notification. Claims are usually filed on Form 1040-X, Amended U.S. Individual Income Tax Return, Form 1120-X, Amended U.S. Corporation Income Tax Return, Form 843, Claim for Refund and Request for Abatement, Form 8849, Claim for Refund of Excise Taxes, or one of the Form 94XX series returns, but may be made in an informal written inquiry. Accounts Management (AM) will expedite the resolution of all disaster claims. Claims include:
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Claims for Credit
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Claims for Refund
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Requests for Abatement
Internal Revenue Manual 21.5.3.4 General Claims procedures states that ‘an informal written inquiry that includes everything necessary to input a correct adjustment’ will be processed.
https://www.irs.gov/irm/part21/irm_21-005-003r
Also, some professional software actually allows for filing of superseded returns. https://support.cch.com/kb/solution.aspx/sw23174
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