As they are in contact now (whether he wants to be or not) then I would add him to the paperwork. As already mentioned, it would really suck if this was the only thing that delayed your case or got you in trouble for misrepresentation. Not worth the risk.
We are in a similar situation. My partners father was a loser and ran out when the kids were young. His mother never listed him on the birth cert, but my partner did know his father when he was very young, and then met him once again when he was a teenager. We have no idea of his address or birthday, so just wrote his name on the form, and put unknown for address and dob. We figure this is ok as he is not on the birth cert and they haven't had any contact for at least 15 years.
I think it is common enough these days for people to have parents who are not, and often never were a part of their lives that the VO's are not going to be too concerned over missing details of parents who were never listed on birth certificates in the first place.