First, you basically need to decide between 4e and not-4e. There is minimal compatibility between 4e lore and the rest. You can always insert bits of lore you like from the option you don't choose, but you do need to choose.
I'm assuming you chose "not-4e" because if you chose 4e it's all one tightly connected edition so the issues aren't really going to arise.
Now lets go on to the basics of how the lore fits together in the rest of the editions.
1e was the foundation of the multiverse and general continuity of D&D lore.
2e expanded and zoomed-in on that lore. It contradicted it in places, but it mostly attempted to expand it rather than overwrite it. For instance, a lot of 2e lore material basically assumed you had access to the 1e stuff and were using it alongside it, or re-printed the important portions to make sure you did. 2e created a huge body of lore. Spelljammer placed all the Material Plane campaign settings in the same Material Plane, and Planescape connected everything else, building on existing 1e lore with a lot more flavor.
3e kept much of the lore from 1e and 2e--except when it didn't. It kept the same
basic structure of the Great Wheel, but it gutted the Inner Planes, rearranged how the Astral and Ethereal worked, and placed every campaign setting at the center of its own multiverse rather than in a shared Material Plane and/or multiverse. At the same time, it added plenty of more or less compatible material that could be used to expand on the 2e lore in the same way it expanded the 1e lore.
5e rebuilt a multiverse somewhere between 2e and 3e, with some 4e inspiration. It put the settings all back into one Material Plane and multiverse. It put the astral and ethereal planes back to pre-3e. It didn't restore the lost Inner Planes, although it expanded on the Inner Planes with some 4e inspiration. With the Forgotten Realms, they tried to do a soft reset of most of the 4e changes, by having actual things happen in the world to put them back. With everything else they mostly assumed the 4e stuff was another multiverse (though they came up with some interesting thoughts in the DMG of how to interpret things in different ways).
Now on to how the Forgotten Realms lore interacts with the rest of it. Because the Forgotten Realms uses the standard multiverse pantheons for the non-humans (elves, dwarves, orcs, etc), most lore about that stuff, even from Forgotten Realms books, isn't Forgotten Realms specific--except when it is. The way you decide that it is Forgotten Realms specific is generally because it contradicts a more general book.
Rarely does this happen before 3e. Most 2e lore about elven deities or what have you from a Forgotten Realms source is pretty much general Great Wheel stuff. Only when specifically mentioning Forgotten Realms history are you generally getting away from standard lore--except when you're not. See, some of those FR books will make it seem like the whole issue with Lolth and the drow happened on Faerun in the past. It may have, but it
also was happening on other worlds if it did. Monsters area bit trickier. Most of them are standard D&D monsters, but there are a few that are unique to the Forgotten Realms. But a lot of the ones that are published in Forgotten Realms sources are
not FR unique. That's probably going to be one of the hardest things to disentangle, is to figure out if something like a Wemic that came out in a Forgotten Realms Monstrous Compendium is actually a Forgotten Realms monster or a general monster. (Spoiler, it's not FR-specific.) The arrangement of the planes in 1e and 2e FR lore is the same as standard D&D, so no problem there.(1) I'll relate some tricks to figure this stuff out later.
Basically, what you have to do is decide on an order of edition priority for lore. I'll tell you how I do it, and then give you some examples of how this played out today when I was working on some of this stuff.
My priority of lore by editions is basically: 2e > 5e > (1e/3e) > (select 4e tidbits)
So I start with lore from 2e books, and see if 5e expands on it in a way that is useful (it often does). If there is a contradiction, I'm likely to say "well, someone believes that" and make the 5e lore in-character misconceptions. It's also not unusual to be able to salvage it and find some ways to make use of it that isn't much of a contradiction. Usually there is no need to go back to 1e lore, because 2e mostly encompasses it. 3e can be useful, but it can also heavily contradict things, so if it says something that doesn't fit it usually gets rejected (unless it's cool and I can find a way to insert it in without a contradiction). 4e gave us the Feywild and made the Plane of Shadow (as the Shadowfell) more significant, and I see no reason not to adopt those.
But that's just the conceptual overview.
What I was doing today was entering information on the Seldarine (Elven Pantheon) into a wiki-like database. I had a variety of source texts open and the Seldarine entry on a Forgotten Realms website. I took as my primary reference Planescape's
On Hallowed Ground. My secondary reference was
Mordenkainan's Tome of Foes--which I used as a list of deities to investigate the lore on
. Starting with
On Hallowed Ground, I then looked at the info in the 2e
Monster Mythology. I discovered that I didn't really need to use the latter book for the elves, as
On Hallowed Ground had the same lore with more flavor. I also had a DnD Gods List file open with the source of information about every D&D deity that has more than a name given to it, as of late 3e.
Here was the order of operations:
1) Look at next deity on the Seldarine pantheon list in
Mordenkainen's Tome of Foes.
2) Look up that deity in the DnD Gods List to see what sources it came from. If those sources were not exclusively for a particular setting (2 appeared to be Greyhawk exclusives and one a Forgotten Realms exclusive) then I've identified that the deity is a part of standard D&D lore.
3) At this point, if I weren't including any 3e stuff, I would eliminate deities that only appeared in 3e books like
Races of the Wild, but it didn't seem to be a problem to fit them in, so I kept them.
4) Read the information on the FR website, and ignore basically anything that contradicts what I read in
On Hallowed Ground. Most ignored information was from 3e, but some was later 2e in FR sources. If it came from a FR source, I might make a note that people in Faerun believe that, but it's not really accurate in my game.
5) If something adds to but doesn't contradict
On Hallowed Ground, use it unless I dislike it for some reason. In the latter case, I might say its one of those things some people in-setting believe, but isn't necessarily true.
6) Cross reference this back with
Mordenkainen's Tome of Foes to see what 5e decided to do with it. Integrate what I like from that, leave out what I don't.
7) Record the lore elements I'm specifically recording in my database (locations of divine realms, relationships amongst the deities, holy symbols, 5e clerical domains, etc), and for the rest just put source and page number references for where I can find more information if I want to.
My version of the pantheon chart (presented in similar visual format to
Mordenkainen's Tome of Foes and 5e style) ended up looking like this:
("Gender" on the chart refers to preferred/most common gender.)
As you can see, I left out a few deities. One was apparently an aspect of another, one has been absorbed (or perhaps their divine power absorbed), and the other left out one was that whole Angharradh crap that I think is an insult to the individuality of the goddesses.
The Core Powers were the traditional set of elven deities. The Additional Powers were the collection of standard elven deities that has accrued over the course of the lore. The Extended Powers at the end were the deities that were unique to a particular world.
If you compare my chart to the original you'll see where my research caused some differences in portfolios and symbols. The Rank is something I had to make a lot of judgment calls on, since 5e doesn't have Intermediate Powers(2), and many powers have changed rank a lot in different products. I came up with my own system for making those decisions a while ago.
Yes, this is a lot of work. Unfortunately, at this point in D&D's history, there is no way around doing something like this if you care about consistency and don't want to limit yourself to a single edition's lore. If you do limit yourself to a single edition's lore (and if you do, I recommend 2e by a longshot), you'll still run into occasional contradictions, but they'll be limited.
If you have the time and inclination though, there is a ton of D&D lore, and with a few upfront decisions you can avoid most of the issues and use most of the lore. Honestly, the lore is possibly my favorite part of D&D.
(1) Do note that this is the source of some of the issues with the Fugue Plain/Plane. FR existed in the same multiverse where the natural order of things is that the deceased drift to the home of their deity or just to the plane that fits their alignment and inclinations best. When the Fugue Plain (originally a location or planar realm in the Grey Waste (and possibly now back to that in 5e, but I don't think they say)) was established, it actually interrupted the more automatic sorting of souls and imposed harsher rules that literally are unnecessary, because other worlds are getting by just fine without them. (My personal way of dealing with it is to say that trapping all of that soul energy is why there are such an enormous number of powerful deities in the Forgotten Realms compared to other places.) 3e, with FR in it's own multiverse can say "that's just the way it is, otherwise things wouldn't work" but 2e FR can't say that because the neighbors are getting by equally well without doing it.
(2) Or demigods as actual spell-granting deities according to the DMG--but then they go and contradict that elsewhere, so I just put in Demipower as a traditional D&D rank for the weakest actual deities.
