I'm seeing a case where an object in my scene doesn't end up in the tome. When I look at it in the umbra viewer it always shows up as culled and when I pick it in the viewer it shows an index of -1. The object is buried inside a bunch of other geometry, so it is indeed never visible. Does umbra automatically remove objects that will never be visible? I wasn't aware of this behavior.
The Optimizer may indeed end up stripping target objects altogether.
This happens when the object is associated to cells that are deemed non-reachable, i.e. cannot be traversed to from any valid camera position.