The objects will remain. You definitely will need some sort of despawn script. Hopefully someone can make one that will destroy all objects. (anyone?

)
The f and file command both do the same thing, but the file command seems to break/interrupt a mission so when you do initiate a different mission another mission is loaded instead of just adding on the 1st one.
Original IL-2 was like this as well. But, old IL-2's dedicated server program hasn't been used in a long time with things like FBDj/daemon/server commander.
@ Troll
I agree with ya. Wish I knew how to make it work for the IL2COD.