Of course there are 600 different parallel Elminsters. In fact there are millions of different parallel Elminsters, because every single DM who has ever run a Forgotten Realms campaign has run a different parallel Faerun, with their own individual different parallel Elminsters. The Elminster that appears in the novels is different than the Elminster that appears in the original Baldur's Gate video game is different than any Elminster that appears in a specific DM's game. Because all of them do different things at different times, different things happen to them, and none of them are affected by what another one does.
I could kill off Elminster in my home campaign right now. Does that mean Elminster is dead in every single other game or property? Not at all. So how could I kill him? Because my world is but one of millions of different worlds that all might be similar but are not exact, as part of the 'D&D Multiverse'. Every single D&D game is a parallel but different world from every other. That's literally what the multiverse concept allows for, and why WotC has pushed forth the idea of the D&D Multiverse. To get across the point that (general) you can do anything you want in your own personal game and it does not matter if it conflicts or contradicts or changes things that have been established in other games or properties previously. Just like people can write whatever they want in so-called "Official" Forgotten Realms adventures and setting books... because a lot of that stuff is ultimately going to be ignored by every individual DM and player if it doesn't work for their game. And in fact, may very well be ignored by other "official" WotC writers in other "official" Forgotten Realms products in the future as well.
And this is why worrying or caring about 'canon' is such a pointless exercise. Because any and all of it is changed and does not match any sort of 'canonical' storyline every single time a new person uses any of it.