Agree that one should not expect to get something in violation of stated rules, BUT....
There is one other aspect that needs to be considered - the OP could not book the L segment online. If it is not possible to book online, thus requiring a phone reservation, the pax can still get 100% credit BUT the agent has to note that in the record - and may not if the pax does not specifically ask for it.
If the original rez was made online, followed by a call to CO to add the CDG-Basel leg, the record will indicate that it was originally an online booking and tech support can fix it so that 100% credit accrues.
If the entire itinerary was booked over the phone it may be more difficult, but it may be worth a call to tech support anyway, since it sounds like the 50% rate is being applied to the entire trip.