The economics of flying is more than just APD. Infact I have doubts that airlines will pass the whole saving onto consumers anyway and just increase the base fare / surcharges.
Flights have to be economic and profitable. If BA calculate they won't make any money then they won't start offering international services from Scotland.
Yes the Scottish Government will have to make up the money from somewhere else. But they obviously feel that reducing APD will create growth in the economy that will more than cover any 'loss' e.g. increasing jobs so more income tax, VAT, business rates etc