To be fair, we may also not need to just write it off as "never happened" (I'm not huge on a lot of Derleth's work, but have some serious respect for what he did to get Lovecraft's work out there after his death). There are in-universe ways to rectify such information.
This probably isn't as hard as it may be otherwise to rationalize, as Lovecraft kind of made it canon that many of the ideas of these beings (what they are, what they want, what they do, etc.) are fractional, incomplete, and wrong. If we consider what Derleth wrote "canon", then it is likely one of these incomplete perceptions of gods and events.
As an example, anything we hear about "Yog-Sothoth" outside of Through the Gates of the Silver Key is an small, localized conception of a completely unknowable being. This is also why the narration never calls the being Yog-Sothoth (except when saying that's what some Earth cults have referred to it as), but instead uses words such as "BEING", "PRESENCE", "IT", and "SUPREME ARCHETYPE".
"In the face of that awful wonder, the quasi-Carter forgot the horror of destroyed individuality. It was an All-in-One and One-in-All of limitless being and self—not merely a thing of one Space-Time continuum, but allied to the ultimate animating essence of existence's whole unbounded sweep—the last, utter sweep which has no confines and which outreaches fancy and mathematics alike. It was perhaps that which certain secret cults of earth have whispered of as YOG-SOTHOTH, and which has been a deity under other names; that which the crustaceans of Yuggoth worship as the Beyond-One, and which the vaporous brains of the spiral nebulae know by an untranslatable Sign—yet in a flash the Carter-facet realised how slight and fractional all these conceptions are." - Through the Gates of the Silver Key
Not to mention the fact that Carter directly ponders that the ideas many have about beings who are vastly beyond the scope of humanity (referring to the Ancient Ones, who are notably below the Archetypes and ultimate abyss) are probably incorrect and as ludicrous as a mammoth seeking vengeance upon an angleworm. They are far too great to care about such things.
"He wondered at the vast conceit of those who had babbled of the malignant Ancient Ones, as if They could pause from their everlasting dreams to wreak a wrath upon mankind. As well, he thought, might a mammoth pause to visit frantic vengeance on an angleworm." - Through the Gates of the Silver Key
One could say that Derleth's versions of events are one of these countless, fractional viewings of things too big to be put into words, hence why they outright contradict the primary source material we have on the greater entities. This would be a relatively easy view to support with the actual text, I'd imagine. You could always point out that Derleth's interpretation goes against and cannot be reconciled with the original author's actual words and primary source material should people refuse to accept that, but I believe it's a pretty reasonable view, and shows how these things are separate from and don't affect the entities at the very top of the food chain.
A lot of the most contradictory stuff is also sorta EU, so there's that.
