What bothers me is that my 20-year campaign and your 20-year campaign may have started out the same but quickly took on the style of the players. We adventured the way we wanted to and created the world we wanted. Now WOTC comes along and changes it so that if I now joined your group we'd be playing in the same game world. It makes the past 20-year exploits in our campaign meaningless.
I can see this. Really, any gaming group has a shared memory of their setting's history. That's what makes it cool to game with the same people for a long time.
There are multiple historic events and nations in my home brew that were caused by previous players. I don't currently play with
any of the players for whom this world was created, and I don't expect to ever do so again (most I don't even know how to contact).
My current group (AFAIK) thinks its cool that the world has history and PC exploits can be retold to others -- so they know their deeds matter. But, I don't want them living in the shadows of the "original" PCs, either, so time moves on.
As far as joining our games (assuming we both did FR up to now), I would say there's a couple of options.
First, I've got my version and you've got yours. I've never liked the Harpers, Elminster, or Lathander so odds are those are all killed off in my version. Loviatar, on the other hand, is cool so she's stolen the loyalties of the drow from Lolth (dark elves, in my home brew, have advanced torture methods so this change might actually have happened, were I to run FR). You, on the other hand, have had Lathander as a major figure who has really increased his standing and the drow are more like insane cultists than anything civilized. How do we "join" our versions of FR?
Second, and more likely IME, is that one of the versions will resonate more with the larger group and become the setting of choice. The less-used one may still have stories told about it, though.
Both of the above are certainly possible, even without the new 4e FR.
Third, we start from scratch and use a new baseline that will grow to reflect our new group. The 4e version is no worse than any other baseline. It may be better because neither of us will be trying to force it to resemble what we remember (at least, we'll be less likely).
If you've got a flavor of the Realms you like, don't change it for your game. If I were to start up a Greyhawk game, I'd use the 1981(?) version, rather than either the Gazetteer or From the Ashes, regardless of the edition. I might pick up an edition-appropriate version of the setting to get some crunchy-bits, but the maps, etc. would be from the version I liked.
I think the 4e FR guide is best for people who are new to D&D or new to the Realms. Sure, you may have some issues with a new group or PBEM, but that's a different issue, IMO, from continuity.
My previous comments don't even mention how much of a cliche it has become to end a campaign setting with an apocalypse so one can start a new campaign in the same world but with new rules. I firmly believe that if one has to tear the world to shreds to make the new rules fit, leave the bloody world alone.
Now, this, I generally agree with. I don't mind tearing things down, etc. But, if it's just to make the 3e flagship setting be the 4e flagship setting, then it's really lame. Release a new setting. People were fans of FR because of its flavor.