Was the version of the 2013 tax return submitted by your accountant online? Do you have a copy of the revised paper version of the tax return? Do you have a copy of the letter from HMRC confirming that they received the revised tax return? When was this exactly?
What is the date of the HMRC letter?
Leave this with me while I draft my answer.
I was aware that once the 12 month window for revising a return has passed, it cannot be revised online and has to be done on paper.
Given that six months has passed since HMRC wrote to you, I think you need to make a complaint. Set out the sequence of events on a piece of paper. Call the tax office on the number here and ask to speak to a complaints manager. Don't let the person who answers the phone offer to help as that has clearly got you nowhere so far. When you get to speak to a complaints manager, explain the situation using your chronological list. I assume that you need the SA302 for a mortgage so you need to impress on the complaints manager the urgency of the situation. In my experience, the complaints managers are good at getting things done which appear to have hit a brick wall so make sure you express your dissatisfaction with how your case has been handled to date.
I did have a case a few years ago where the HMRC computer wouldn't accept a revised tax return even though the revision was within the 12 month window. There was clearly a technical issue on the HMRC computer and my client's record so HMRC cleared the initial incorrect return, I gave it a couple of days and then I submitted the revised return. You might mention the possibility of clearing the original return to the complaints manager as I would be worried that they have mislaid your paper return.
I'm afraid that there are no easy solutions and you will just have to go through the complaints process to get your problem resolved.
I hope this helps but let me know if you have any further questions.
Keep a copy of everything you send to HMRC. Contact them again on the phone if you don't hear back from HMRC within a month.