I did not submit the modified W-2, will paper submit with the original W-2. Still, it would be nice if Turbo Tax could fix this issue that it appears they are aware of. From others comments, it sounds like this situation (over pay 401K, obtain the excess and submit a 1099-R) didn't generate problems in previous years of the software.
Or as
@viveks45 pointed out, refund the efiling fee already paid for.
