The gaskets (seal #13 & 14) are seated in the lid and lower airbox. I never replaced them, so I don't have a clue if they are glued in there, but they never fell out during air filter changes either.
It might be easy to pick them out with a dental tool or awl, or might be a serious pain in the butt to get them out, clean the bottom of the groove and install the new ones w/o getting them twisted or damaged. Yamaha usually likes these to just be a press fit, so it's probably not that bad to remove them and only a little fussy to install the new ones. Likely getting the final seat when you screw the 13 screws back in to secure the air box lid.
(I wonder why something they would like is to check so often is so over secured? My old Ducati just had spring clips like cars used to have. The new Chevy in the garage only uses 4 screws.)