Flush rivets are countersunk rivets, they will be there next to the A3 rivets you couldnt find. Have another mummy look.
What I do is get everything thats in a plastic bag like nuts, bolts , rivets etc and stick them up on a board with drawing pins, lined up with each box they came out of. if you take it off the board you mark the board where it was so you know you actually had it. It works, all the little bags are there to see, no searching. Honestly every person who has built a kit (including myself) has sworn there's something missing, only, embarassingly, to find it later on down the track.