What else would you count except for everything? Who gets to decide what gets considered "valid" research and what doesn't? No matter what you do, factions of the obsessive collector brigade are going to be pissed off for changing what's been written in some book.
Well, the rule is that if sources contradict each other, newest Realmslore always "trumps" older stuff, right? For example, a Dragon article lists Alusair as FTR 20, but FRCS has a "corrected" stat set which trumps the Dragon article. And it's not the only case in which an accessory or article has updated previously published lore. Now, if I write a new adventure series about Marco Volo, I might change his stats completely and maybe even swap his class to ranger, and regardless of what some "obsessive collector brigade" might say, that would be the new "canon" (if it slipped past in editing; and such slips surely happened often in TSR). Of course, this might be "corrected" later on, but it's what you roll with for some time, unless you want to ignore his new "canon" stats.
I'm not sure I get your point about "valid research"... isn't it quite obvious that you look up which sources (books, novels, articles) may contain information that is relevant to what you're writing? For example, if you're writing an adventure in Cormyr, you might take a look at campaign settings, Cormyr-module, Four from Cormyr, Volo's Guide to Cormyr, Cormyr: A novel, etc. Likewise, if you're including stuff about the Eldreth Veluuthra in your article/accessory/novel/short story, you should take a look at Cloak & Dagger and Champions of Ruin, at least (and in this case CoR always "trumps" the lore in C&D). And so on. It isn't too hard to narrow down the list to sources that have the information you need for the level of details and Realmslore you're intending to use.
As for the changes, and people being upset, I know a lot of people were p****d off at the design team for not following up on such 2E plot hooks as the Manshoon Wars or the Rise of Iyachtu Xvim (Xvim and his followers were a major threat in my group, and we were not happy about Bane just popping back into the Realms with a parlor trick) -- that didn't prevent them from playing in the Realms, however, because it didn't change things a lot in the big picture. Sure, they dropped the ball with the best hooks, and introduced others that made little sense to many, but at least it was still more or less the same Realms.
Change isn't bad, if it is logical; the events of the Spellplague are not, at least by my standards. You see, I think they took the "lazy" option in it all, saying: "Let's reboot everything with a huge magical catastrophe,and let's leave the details out... well, we don't need to think too hard about it, because it's *magic*, after all". When people started to point out inconsistencies on the message boards, they replied: "We're not retconning anything, because as far as we're concerned, it always was that way." Sure, I wonder how SW fans would feel if Saga 2nd Edition removed the Light Side of the Force and rendered all Jedi powerless ("Look, the Dark Side is a power of its own, separate from the "Good" Force, and that's why the Sith still have their powers... as far as we are concerned, it was always that way!").
As an aside, Eberron's only been out for 5 years, while FR has existed since the tail end of 1e (87? 88? so over 20 years). And FR was the flagship setting for the bulk of that. If the two have the same amount of "quality" lore, than maybe FR deserved to get blown up.
Yes, FR was the flagship for TSR, which practically meant that a lot of products got the FR logo slapped on them ; some didn't have anything to do with FR (such as the Great Khan Game), while others were more or less succesfully "Realmsified" ("Hey, we could publish that adventure in the Realms... hmmm... what's that country? Cromyr? Kormar? Something like it. Yeah, that's what we are gonna do!"). More often than not, the products contained contradictory lore or were clearly just dropped into FR without necessary research and changes.
And this publishing policy and sloppy editing/attention to internal consistency resulted in holes a Netherese city could fly through; which meant that such authors as George Krashos, Eric Boyd, Steven Schend and Ed Greenwood has their hands full in trying to patch it all up in the final years of TSR (and they did a remarkable job). Most of the 3E stuff is "decent enough", and anything done by the Lorelords mentioned in the previous sentence is excellent in quality (by my standards). As far as I'm concerned, most of the AD&D stuff published by TSR does not compare to their work or Eberron stuff (based on what I've heard from friends who run Eberron). Now, the last I counted Eberron had something like 40+ or 50+ accessories published so far, plus quite a many novels and Dragonshard articles, to boot. That's a lot to read, surely, but if I wrote an article on House D'Cannith, would I really need to read *all* of them? And even if I did, I think it's not much less than reading the most popular and up-to-date FR accessories and articles.
Anyway, I don't think an occasional "bad" article or book merits "blowing up" the setting -- especially if later on the published stuff will be "corrected" (such as in the case of many inconsistencies in FR).