Thank you MaryK4: I ended up finding how to use the correct taxable amount in for 1099-R, box 2a, and TurboTax was excellent at navigating me to a Form 4852. I attached the VA letters of withholding and on Lines 9 & 10 of the Form 4852, was able to detail exactly why the 1099-R, box 2a, amount should be adjusted. All the correct calculations flowed properly and my reduction in income was recorded properly. I thought it best to mail in my return because I still owed. Your other suggestion about using a negative value in "Other Income" to offset the 1099-R, box 2a, amount, is a good idea, however, I thought the cleanest way and more explanatory was to go with option one using the Form 4852. Besides, I had already completed my return using the first method. Your information to me was very helpful and gave me confidence that I didn't have to file, pay, and then refile an amended 1099X return. This should work out and I would definitely be able to survive any questions about the way in which this was finally done.
