What is different about the original and second 1099-R? Specifically, what is in box 1, 2a, and the code(s) in box 7? And, if box 1 changed, how much did you actually rollover, the amount in box 1 of the original 1099, the new 1099, or something different?
I believe I know the answers to your other questions, but I don't understand why or how they issued a new 1099-R. Even if the contributions were ineligible, they were still there, and part of the withdrawal/rollover. I want to know more about that before I answer the rest.
@dmertz
