You will probably have to re-do the hierarchy of the model. I've noticed when I've done POF->COB conversions in the past, I've needed to remove everything from the 'Freespace model' level; and also the subobjects end up with their centres out of place, so they've needed to be unglued from their lights, and reglued in the correct positions (thats basically what happened to me when I did the Hades, all the gun barrels had their centres in the wrong position and ended up rotating in a weird manner. Didn't realise until after I'd done all 60 turrets, so I just deleted the barrels.)
Alternatively, if these new Vasudan models happen to be the ones that I built for you, then I could just send you the final .scn files I have, with all the hierarchy set up correctly, so all that you need to do is convert them back to pof.