The cosmology changes for FR between 2e and 3e are largely a matter of semantics. There's still Limbo, but it's called the Supreme Throne. There's still Gehenna but it's the Blood Rift. Etc. All of the various outsider races are still there, by their same names. Very little of substance changes.
Yeah, I've done a lot of exhaustive research into the nature of the planes in FR's cosmology recently and that's simply not true. The 2e and 3e planes don't match up as neatly as you're describing.
For example, is Gehenna the Blood Rift or is it the Barrens of Doom and Despair? Both planes share characteristics of 2e's Gehenna, including inhabitants, terrain, and overall alignment. Exactly where did the Outlands go? Are they Cynosure, which is supposed to be a single hall? Where does Mechanus fit in? What about Carceri?
People, I think, are more forgiving of changes like these because they made FR more unique, not less unique, which I understand. That doesn't mean they weren't huge changes.
Between 3e and 4e however it radically changes. Entire planes vanish and new ones appear. Entire outsider races vanish and have never been there, while new races appear, sometimes hijacking the names of previous and completely different races. The cosmological origin and backstory completely changes.
This is partially true but not entirely. The planes of 3e, for example, are more less there, with a few name tweaks and relocations. The Abyss has been moved to the new Elemental Chaos (which also includes the traditional elemental planes) and the Astral Plane is now the Astral Sea. And a few of the Outer Planes have been destroyed (Heliopolis and Dweomerheart, most notably). That's about it, though. Everything else is just a renaming and in this case they
are just renamings.
As far as I know, none of the outsider races have vanished - they've either just become de-emphasized or reflavored. Yugoloths are now a kind of demon (not a change I'm a huge fan of it but it's also not all that extreme). There are now two different races called archons (again, not a huge fan) but that's just confusing, not an example of the celestial race being eliminated. Eladrin now come in two varieties, which again, is confusing, but not a disaster. But again, most of everything else is the same.
As for the cosmological backstory changing, I assume you're talking about the primordials (which, BTW, were originally an invention of Greenwood's for his home campaign) and the existence of Abeir. Sure, these are retcons, but neither of these is any larger than the discarding of the Great Wheel or the Time of Troubles. Not by a long shot.
Also, IIRC, Wood Elves in faerun are largely descended from Moon Elves; So in 4e either Elves come from Eladrin, or thats another retcon.
Correct, elves originally descend from eladrin, who came over to Toril from the Plane of Faerie millennia ago.
Its a completely different setting with a few borrowed characters, as opposed to the same setting, but updated with some changes.
That's your opinion, not objective fact.
My opinion (which, again, is not fact) is that WotC went overboard on its attempts to fit FR into the 4e cosmology and lore, but I also don't think any of it is irreconcilable. I'm not a big fan of all the changes (mixing up the names of races, compressing the cosmology), though I am of others (I like the Elemental Chaos and Astral Sea, as well as the elemental vs. immortal conflict).
I imagine that a 5e FR, reacting to the reaction of 4e FR, would probably involve some backpedaling. But I don't want to see
all backpedaling.