For god's sake... Unless you do this serially, the airline may most probably not even notice you're doing it. About short-checking luggage, it's your luggage and your call. If a check-in agent doesn't want to do it for you, call the supervisor and remind them of this fact. A stopover fee cannot be charged for this, since a stopover has nothing to do with luggage, it is simply a layover of >24hrs. The fee that was quoted further upthread was most probably an 'admin fee' for having to retrieve the luggage from the baggage system (it had already been through-checked).