I think I would tell the dad you need to be in contact with CRA to figure out how to move forward since you have already issued a receipt for the full fees and therefore can only issue a duplicate receipt (marked duplicate).

I don't believe you can issue a new receipt but at the same time technically you likely had to issue him a receipt for the time he was in the picture (a joint receipt in the least) and since you didn't you will need to figure out from CRA what to do.

It was on both the parents to deal with this on their end. Separation or not they both needed to know who was claiming what and make sure they didn't double claim.