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The tmd preset files are usually identified with a suffix like '_clean.tmd', '_takeoff.tmd' and '_landing.tmd'. A preset file is loaded after the (main) .tmd file when the aircraft is placed onto the runway or set into final approach or somewhere on the map in the air. The preset then overwrites the default values of the (main) .tmd file. This way when the user selects the air start, the gear is already retracted and the flaps are set to up even if the gear or flaps where down before the location on the map was changed.
It is recommended to pay attention when the presets are created, it does not look good if the gear lever moves into position only after the aircraft was moved up in the air or if half of the cockpit switches change their status in the first brief moment. Especially slow elements like the gear position or flap position should be adjusted correctly so that the aircraft doesn't fall from the sky on final approach or that the user has to wait for the flaps to extend when he/she wants to take off.
Not providing a preset for a particular initialization method is possible, then the Aerofly just won't change any default parameter of the .tmd file. Some simpler aircraft might not need a preset for all of the different initialization modes.