| I fully understand your situation. Since, the option of asking Dad's company that reported the 1099-Misc is not available, I would have written to the IRS and told them that the 1099-Misc was incorrectly reported on your SSN and instead should have been reported to Dad's tax return.
By the way, how much was the amount reported on the 1099-Misc?
A letter from Dad to the IRS attesting to this fact would also have been helpful. However, the IRS would then want to know how this error occurred! Your Dad probably provided your SSN to the employer so as to report the income on your tax return!! I think this could have created some problems for your Dad, in my opinion.
The approach that your Dad has taken, whilst from a tax liability it has not impacted your tax return, it is technically wrong. To file another amended tax return is very problematic, however, if your are still unconvinced, this would be the time to visit your local CPA and get his written opinion as to how best to proceed for you.
For the future, I think the best approach would be to tell your Dad, that you are uncomfortable with reporting any income on your tax return so as to avoid this problem for both of you in the future. Your Dad's employer should get the SSN corrected immediately and this should solve the future problem. | 
