Well... not exactly. DVD! was never released under the Planescape product line, and deviated pretty seriously from what Planescape was. You could just as well call it a Ravenloft scenario.
The issue with it not being released under the Planescape line was that WotC (which had acquired TSR a few years prior) had determined that product lines - that is, the appearance of campaign specific logos on the the cover/front of a product - tended to narrow the target market they were aimed at. As such, it had been dialing them back for years.
It's no coincidence that Warriors of Heaven, Vortex of Madness and Other Planar Perils, and Guide to Hell didn't have Planescape listed on them, the same way that Die Vecna Die! didn't. Likewise, Bastion of Faith didn't have the Greyhawk logo despite being about Heironeous and Hextor, Carnival didn't have the Ravenloft logo despite being about a Ravenloft-specific organization, etc.
Likewise, I'm not sure how you could say that it "deviated pretty specifically" from what Planescape was. Harbinger House was a Planescape adventure that dealt specifically with deities in Sigil (using the work-around that some mortals were ascending to godhood while in Sigil), and had an item that specifically kept out the Lady of Pain's awareness. Likewise, Dead Gods has a god (or rather, some pieces of a dead god, that still have some awareness) in Sigil.
The major point that most Planescape fans seem to find upsetting is that it shows the Lady's limitations (she can't instantly force Vecna out), that it implies that she has a "true, resplendent form" (which it says she'd have to take to battle Vecna directly), and that she speaks aloud (to repair the damage done to the planes by Vecna's time in Sigil). Even the latter isn't without precedent, as it's implied that she speaks directly to Duke Darkwood at the end of Faction War.
Most likely, it was the module for the Generic AD&D line that updated from 2nd to 3rd.
As you noted, the module for "generic" AD&D to be updated to Third Edition was The Apocalypse Stone. Die Vecna Die! is pretty clearly meant to be an edition-changing event for the whole of the AD&D multiverse, even if it can't deal with every campaign world specifically.
Also worth noting is that the proposed changes to the settings laid out in the appendix never happened whatsoever (though some were sort of awesome). It also didn't touch on Forgotten Realms, but rather Greyhawk.
I need to go back and reference what those changes were, but some of them did happen, and others were plausible. The idea that the "half-worlds" of Tovag Baragu became multiple, parallel Material Planes is indeed something found in Third Edition, which now has multiple Material Planes as its default assumption. There are also far fewer Inner Planes now (no more quasi- and para-elemental planes, for example, in the Third Edition Manual of the Planes), though we admittedly aren't told anywhere else that any of them "ran aground" on a Prime Material world.
Depending on how you take MotP's existence of things like the Plane of Faerie or the Plane of Mirrors, you could also say that there were new Outer Planes being introduced (though to be fair, I don't recall any Outer Planes being lost).