Last year I was in the position to book hotels for colleagues who do not have corporate cards and who do not travel so often. I booked the hotel room, told them how to check-in to get my elite benefits, and in most cases I got the points/credit for those stays. Where this did not happen, the hotel advised that the traveller changed the FFP number. I did not (and I never would) go back to the person to question that, and I would like to believe that this is also what your boss would do.

This being said, I suggest you do exactly what was advised above, and see the effect. If asked by the boss, you can tell him that the hotel changed it at check-in, or you can play innocent. He is in breach or rules, so in essence he can't complain that he did not get points on hotel stays where he did not stay at the hotel.