We know from Vegapunk that Joyboy was a man from the Great Kingdom born 900 years ago at the start of the Void Century, as well as the very first pirate in history.

Going by the attitude of the World government today towards the pirates, the 20 Kings and Imu would have done all in their power to defeat Joyboy both at war as well as his ideology of being the freest man on the seas. The most symbolic way to do the latter would be to burn his flag or the Jolly Roger in this case.

I believe that while they were successful in defeating him, as evidenced by the fact that Imu apparently has Joyboy’s straw hat as a trophy, they were not able to erase his ideology as we still have pirates today.

What I think happened was that they were able to destroy Joyboy’s ship in the war but were not able to burn/destroy his Jolly Roger. So while the ship was destroyed, “one piece” of it remained and thus the name of the “treasure” as it symbolizes all that pirates live for. And that is what Imu and the World government hate so much and are doing everything they can to prevent today’s pirates from getting their hands on.

During the run up to Laugh Tale, maybe the Strawhat pirates’ Jolly Roger would be damaged by the World government and when Luffy returns from Laugh Tale, he is now flying Joyboy’s Jolly Roger along with his own much to the chagrin of Imu and the WG. And that could be a flag that the entire alliance against the World government could rally to during the final war.

Judging by the fact that Luffy has inherited both his fruit and his will, if Joyboy also “designed” his own Jolly Roger then it should be something wacky like the original Jolly Roger that Luffy made, which would explain why Roger laughed.

Also, maybe Roger laughed because he spent so much time thinking they would be the first to discover this final island. Only to discover someone else’s Jolly Roger planted there.