The problem with cars in Boiling Point is that the game can only track five "left" vehicles on the map. Normally when you leave a vehicle you can see it on the map (with an icon saying something like "Left Vehicle N1"). Sometimes, entering a vehicle will cause the counter to loop round, and make an existing vehicle on the map "disappear".
The main thing to do is to make sure you save before entering a new vehicle. There are a few potential solutions if you notice your favourite vehicle disappearing - basically reload, return to it, carjack something else within 200 metres so it drops off the map but doesn't disappear, then get back into it thereby "refreshing" it with the game in a new slot.
Having said that, once you can fly around in combat choppers and speedboats with machineguns, it's tempting to just use those all the time, and scuttle them when they run out of fuel / health (they can't be fuelled, rearmed or repaired) to get a new one. As long as you don't complete the missions that actually give you those vehicles, and as long as you scuttle them sufficiently far away from their spawn points (at least a few km) you'll just find a new one at the spawn each time.