Hi Bill,
I am sure you're not looking forward to removing that floor ... having only had to pull 3 rows back out when the nailer decided to fire over already nailed flooring!
I put a bi-metal blade in my Harbor Freight Oscillating tool and cut all the nails (yea, I used a LOT of nails) by sliding under the flooring and above the rosin paper. I was able to remove the individual boards without top surface damage, and was sure to tap down any remaining nail pieces in the subfloor before replacing the flooring. And yes, the nailer was put in nailer-jail for that misdeed (kept it off finished flooring from then on!). Replacing the rosin paper in damaged areas was easy enough.
Glad you got the situation ironed out.
Good luck,
Rick