What happens to custom vehicles if the impound lot is full?

Solution 1:

In GTA Online, vehicles will only save if you attached a tracker to it at a Mod Shop. Without a tracker, the game thinks it's just another car that you stole and it will not save it. There is no way to get that vehicle again, so you're going to have to find another tow truck.

It is also impossible to prevent a car from getting impounded. If you get a wanted level in a vehicle and die soon after exiting the vehicle, the police assume it is yours and will impound it.