The only issue I see with amending is that Form 1040X generally takes the place of Form 1040 (with Form 1040 being where the normal ROLLOVER indication would otherwise be present) leaving no place other than the explanation area of Form 1040X to indicate that the distribution was rolled over. It seems that your explanation has already been provided and accepted by the IRS, so it's possible that the amendment would just end up getting rejected because it shows no change to the information that the IRS already has with respect to your tax account. If things are already in a good state at the IRS, documented by the letter that the IRS sends when a situation is resolved, it may be best to just leave things as they are.
