Here's what Patrick Dimmitt, ex-IRS, said today on this topic on the NAEA Board:

Note that the IRS treats an amended return filed before the due date as a superseding return.  See IRM 21.7.9.3.4 and IRM 21.7.9.3.  If you are filing the superseding return on paper using the original form, mark the top of the return "Superseding Return" so it is identified as such.  For individuals, efiling is limited to amended returns.  Again, an amended return filed before the due date will be treated as a superseding return.  If you want to file the superseding return using Form 1040, it must be done on paper, and again, mark the return at the top, "Superseding Return.

Note if a return is filed by the unextended due date, a filing after the original due date will not be considered a superseding return even if there is a filing extension."