Well, that is a crappy, but avoidable problem. Just tell the desk when you check in that you need to update the HH number with the stay. Only takes a second.

As far as your boss not finding out, well that is unlikely if he/she pays attention to that level of detail.

My question to you, is it policy that your boss gets the points? If not, you won't be doing anything wrong technically which means you can get it away with it until your boss notices and then just apologize and stop. (Assuming you want to keep your job...)