I don't actually have Truespace installed and so can't actually mess with the cob. However, I see one major problem (which may compromise the beam-intersect code on a deathroll or something like that) is that the hull geometry (Guardian) is not the root of LOD0. The cob heirarchy has to look about like this:
Model
----Guardian
--------Guardian_geometry
--------Guardian_detail
------------Guardian_detail_geo
------------Loc Light
--------Loc Light
----Turret01
--------Turret01-geo
--------Loc Light
...
when it should look like this:
Guardian
----Guardian_geometry
----Guardian_detail
--------Guardian_detail_geo
--------Loc Light
----Turret01
--------Turret01-geo
--------Loc Light
...
In other words, all the turrets and the lower LODs should be children of the LOD0 geometry, not siblings.
If you redo the heirarchy so that the actual hull is not considered a seperate subobject from the phantom hull you've got now and reconvert, you'll instantly fix the bounding box issues. Now that may or may not have anything to do with why hitting it with a beam makes it crash, but without geometry in LOD0's root I could envision the game trying to hit a vertex on the "hull", not finding any, and dumping out. Or seeing the collision check for the beam intersection die when the boundingbox max and boundingbox min are equal. Try it and see if it helps.