I am surprized that you could get the screw out of the barrel without clamping the barrel. If the pin is not moving, it may have shoulders on it or be press fit into the hole.
When I cut a screw off, the end is a little jagged. Rather than trying to smooth the end with a file, I insert the ragged screw into the threaded barrel with some red Loctite turning it into a T-nut. Afterward only the "good" screw can be removed from the barrel. When putting #6 TORX tools on either side of the screw set, only one screw can come out.
You can see a screw set in my photo as well as loose screws and loose barrels. The bolt cutter is at the top of the photo. There is actually a #2X56TPI Gold plated screw protruding from the cutter. The upper plate on the cutter is threaded for various sized screws. The lower plate has clearance holes. When you squeeze the handles together, the screw is sheared off. I usually buy long screws and cut them to length.
When you say that one of the screws is starting to strip, are you talking about the male thread, the TORX recess, or the threaded barrel?
It doesn't matter if there is a little space between the tips of the 2 screws. You just don't want them touching because you lose the ability to get rid of the rattle.
Can you send some screen shots of your knife and the loose parts?