Also check 
I think what's more likely to have happened is that Pochita has gained sufficient faith in Yoru to give her (figurative) gun back. Her initial goal was to force this to happen, but she has become increasingly resistant to the idea while simultaneously growing an actual affection for Denji (and for Pochi by extension).
Plus, just because Makima explained his powers to us doesn't mean that she actually knew everything about them. She was just his biggest super-fan and had a very obvious god complex, which makes it make sense that she would be overconfident about her knowledge of this topic that almost nobody else knows about. It kind of seems like only Pochita, if even him, actually knows how his erasure power works, or even how to reverse them.
It's also possible that she was totally correct about his power, but failed to realize that things which were erased from the past can still be rediscovered again. As a commentary on the nature of propaganda/control, I think this could fit the overarching narrative quite nicely.
My third and final theory on the matter is...a bit more silly. More of a reach too, I think. When we eat things, we eventually expel them, right? Could just be that nukes were gone for long enough that it is now their time to kiss the porcelain throne.