As long as you have proof that this was rolled over, go down to line B2 of 1099R worksheet 3/4 way down and enter the amount rolled over.  This would be the total less the tax withheld.  Because that is the only amount eligible for rollover.  And keep proof in your file in case questioned.  So taxpayer will end up with taxes paid in for no income reported except the amount of withheld taxes themselves.