The amendment must be filed on paper and mailed to include the manually prepared amended Form 8606.
The as I've said several times before, line 1 of the amended Form 8606 will have a zero on line 1 because with the contribution returned there is no contribution to report. You'll also have a zeros other lines in part 1 where you previously had non-zero amounts. Leave line 6 blank since it's not involved in any calculations on Part I.
