I've seen this with some TBP ships while I was readying them for use. You can fix it without reconverting the whole model, but it requires doing things the hard way in PCS. PCS has the ability to create and edit thruster points, but unfortunately it won't show them to you. So, you need to create a dummy primary firepoint and place it where you want your thruster point to be, then copy the position into the thruster point's location field. Then, relocate your dummy firepoint to the next location and so on. Just remember to delete the firepoint when you're done. Unfortunately, this problem may not be restricted to thruster points. The TBP ship I was working on was a fighter, and I noted that all the primary and secondary firepoints were out of position in this manner when done in ModView as well. You may need to edit the turret firepoints in PCS to make 'em match up properly.