The Numidium wasn't exactly destroyed, it was trapped in an alternate timeline where it was caught fighting the Altmer all the way into the Fifth Era. The entire premise of Landfall is that the timelines are merged after the Jills repair the dragon break, and after having destroyed Alinor, Numidium proceeds to destroy all of Nirn. To quote a response from r/teslore, "Arniel Gane was a fool who didn't know what he was doing. Saying he replicated the experiment is like saying someone squeezed some hydrogen in their hands and replicated the Sun. He was working with a warped soul gem and only one of the three tools, and that singular tool was also broken. He didn't replicate it at all. And it's pretty clear where he went! There's a reason you can summon him after that quest: He latched onto you."