You're not going to just amend to "turn off" the Roth going forward?
Does the W-2 for the employee show Roth deferrals, or pre-tax?
I'd go in under VCP - tell the IRS, hey we never expected there to be Roth, nobody (other than this guy) even asked about it, etc. If all your other documentation supports the fact that the document was done with the mistake and there was no other expectation, they might give you the okay. I guess there's some difference to the appeal you'll make, depending on the rest of the fact pattern regarding how those amounts did go in.