I think the issue is that Form 1310 can only be filed with a Form 1040, with Box C checked. If boxes A and B are checked, the return must be filed with Form 1040-X or Form 843. I believe this is the case, whether the return is filed by paper and mailed or if it were filed electronically.
According to the IRS rules, if a personal representative is filing the final income tax return, on behalf of a decedent, Form 1310 is not even required. For that matter, the person just needs to indicate that they are the personal representative, mark the return with "DECEASED" on the top of Form 1040, and send the return by mail, along with the court-appointed documentation.
Otherwise, IF one inadvertently happened to send the original return electronically with Box C checked, since the IRS allows 1040-x to be e-filed with the Box A or B checked on Form 1310, one could electronically file the amended 1310 form (with only Part I completed and Box A or B checked), subsequent to the original filing. This would establish, for the record, that a personal representative did, in fact, exist. This will require that you include court documentation. Some software applications will allow you to attach a pdf to a return, before efiling, similar to what was required with Forms 8915-E and 8915-F last year and this year respectively.
