Vegapunk did not create the weapon that was used to eradicate Lulusia.
As we can see in Chapter 1086, Dragon and Ivankov rule out the possibility of Vegapunk having created the weapon. Dragon knows Vegapunk well enough to be certain that he wouldn’t create a “dedicated killing machine.” This is shown by the nature of their conversation in Ohara.
This interaction shows that they were well-acquainted before Dragon even founded the Revolutionary Army. But then why does Imu explicitly state that it is time to put “Vegapunk’s invention” to the test?
I think that Vegapunk’s invention, the Mother Flame, is in fact the energy source that was used to power the ancient weapon and not the weapon itself. There is further evidence which suggests that an ancient weapon was used.
Dragon’s question of “why wait till now to use it?” is answered quite simply by this theory. Vegapunk had not yet invented the energy source.
We know that Vegapunk has been researching power sources. Lilith said Egghead’s tech was powered by “fire” and spoke of a hypothetical “eternal flame”, while Stella’s dream is to find an unlimited power source. All this alludes to the Mother Flame being an energy source and not a weapon.
But if he has invented an energy source capable of powering ancient weapons, then why does he say that he is getting closer to getting the power source that ran ancient machines? Hasn’t he already done that with the invention of the Mother Flame?
As Jinbei mentions, Vegapunk is a perfectionist. He considers Momo’s fruit a failure just because the color is different. I think that the Mother Flame is not the exact same power source that was used in ancients times, it is a slightly worse replica.
The Mother Flame is similar to Momo’s fruit in the sense that it accomplishes its main purpose, but it is not quite an exact copy. This is why Vegapunk says that he is getting closer to getting the power source used in ancient times.
TL;DR: Imu eradicated the island of Lulusia using an ancient weapon which was powered by Vegapunk’s invention, the Mother Flame, an energy source similar to the highly advanced energy source used in ancient times.
Theory by AllBonezSkeletor (https://www.reddit.com/user/AllBonezSkeletor)