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But then you would lose your war factory because the flying vehicle gets stuck on the lip.
Using the jump jet locomotor prevents that problem.. did you read the first post?
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Would it be possible to make a special war factory, like a helipad, that you build the flying apc from?
VehicleTypes can only be build from the War Factory, just like AircraftTypes can only be built from a helipad. VehicleType and AircraftType both support different logics in the game, but the best one to use for air transport, is the VehicleType - only buildable through a war factory..
I believe I already mentioned having a sparate war factory for flying-vehicles, using the same technique we use for making a Naval yard in TS
(basically, making a dummy house for just the naval units, so the game thinks it's a "captured" war factory)