The collsions are stored in tree.klz
In your case it's a steady collision, meaning it's only stored in tree.klz without any link to another file (like scene.4ds or bin files)
I was trying to remove a litttle Stop signs (see attached images) on the Tutorial mission.
I planned to let enemy reinforcements drive through that barrier.
I could make the barrier open by adding a definition to it, but the sign sticked to its position, so i removed it in the scene2.bin file.
But the collision was of course still there. It blocked all incoming vehicles..
So i searched with a HEX Editor (with range mode) for the position values and i moved it 10 meters to the left (position B), thought the problem would be fixed now.
But it seems there's even more to edit in that tree.klz
Now if you walk into the stop sign (original position A) you get magically transformed to the new position B.
As you see the klz file is very complex and without an editor impossible to modify.
If you have a model in scene.4ds (e.g. name NewModel00) and this model is linked in the klz file you can remove that collision by just hiding your model in the bin file.
http://hd2.wikia.com/wiki/Entities#Common_Attributes
As you can see if you add block 3340 it will hide the model and as its linked in klz also the collision.
But i have not tested it yet. And of course it does not help to remove steady collisions..