This is probably old news, but a book in the Dragonborn expansion mentions that Azura instructed the Tribunal+Nerevarine how to sever the Dwemer's connection with the heart. As a result, their "stolen immortality" was taken away and they turned to dust.

This would indicate that the Dwemer did not do anything, but that they were killed by the Chimer/Azura.

Other books say they used the heart, and went into Numidium. Who's right? Well, we know Numidium has been activated, and thus that the oversoul of the dwemer is inside, that the Dwemer tried a Walking Way with him...

lol. You talking about Nerevar at Red Mountain? Yeah, that book has been around since TES:III. Its only one take on the story though, that's why there is so much ambiguity surrounding their disappearance. For example, both http://www.imperial-library.info/content/battle-red-mountain and http://www.imperial-library.info/content/kagrenacs-tools claim that Kragrenac used the tools on the heart himself, not Nerevar at Azura's instruction.