You know those games where you try to get the little ball bearing to go through a maze so it will drop in a hole to win? With you situation it would be theoretically possible for the bolt to migrate to the head, if you balanced the bike on its front tire (maybe take off the fender first), with the rear tire directly over the front tire, then shook the bike up and down for 5 or 10 minutes.
If the OEM exhaust are intact and unmolested you'll
never get 'em out and they won't get to the head.
If you really dislike the rattling you could drill one baffle tube in both the forward & rear baffle and then spend hours trying to get lucky jiggling the exhaust over your head, behind your back and such.
You could increase your odds by drilling all six outlets total for both baffles. But then it's so unlikely.
Your gonna have to live with occasional rattling otherwise.
BTW By your procedure description your cut-offs are inside the rear half of the rear baffle. They won't hurt anything if you leave them other than being tossed around with exhaust flow.