I think you should contact Lufthansa to have them give you the points. It is the airline that is buying the points from the frequent flyer programme, and as such they should be able to buy some for you. Not sure what their policy is though.

Had a somewhat similar incident on LH myself on Thursday. Was booked MAD-FRA-SZG, but ended up flying MAD-MUC with a rental car to SZG. Let's see if they want to give me the 2500 miles for the missing segment...