Warhammer has races that silently disappear between editions. What happened to the Fimir?
They made a recent appearance in the Graham McNeill Sigmar-era novel Empire. The 'mist daemons' are never definitively labelled as Fimir but it is very clear what they are supposed to be.
The Chaos Dwarfs in the Warhammer Fantasy world have also simply disappeared. To the point that even though they are still included in the last official Blood Bowl rulebook, they are the only official race not in the computer game.
They were mentioned, repeatedly, in the second edition of the role-playing game.
They are still mentioned quite a bit, both as a source of equipment for the other chaos factions and Ogres and as the origin story of the Black Orcs.
It seems likely, in-universe anyway, that there's simply too few Chaos Dwarfs to make a full army out of them, even with Hobgoblin and Orc slaves supplementing them, as the scarcity of their race was something mentioned repeatedly.
Chaos Dwarfs have seen a resurgence as of late 2011, given that Forge World has started producing a line of them in Warhammer Forge. Whether or not they'll return to being a mainstream army is yet to be seen.
Chaos Dwarfs were added to the Blood Bowl video game in its second expansion in 2012.
Bull Centaurs have it even worse. Chaos Dwarfs have three models being consistently produced as Hellcannon crew (admittedly without the stylish headgear of the classic Chaos Dwarf range). Bull Centaurs have vanished entirely.
Malal, the fifth Chaos god, was dropped around the 3rd edition of Warhammer Fantasy. This happened because the people who held the Copyright left Games Workshop. An entity called Malice, a Suspiciously Similar Substitute, has since appeared in Warhammer 40000, however. In addition, Be'lakor the Daemon Prince in Warhammer Fantasy share's many attributes with Malal.
In Warhammer 40,000 the Squats vanished as well, partly for low sales but mostly because they were too silly/campy in a setting that was becoming Darker and Edgier. Word of God has usually been "the Tyranids ate them all" (supported by the "Abhuman" section in the 6th edition rulebook) but they have occasionally tried to claim "they never existed". Blame Chaos, perhaps.
The same happened earlier on to several models in the 40k range with the simplification that happened in the 3rd and 4th editions. However some of them have been making a comeback in recent editions, most notably Bjorn the Fell-handed and the infamous Jokaero.
Another prominent example are the Illuminati (possessed psykers who manage to overcome the Daemon that possessed them, eventually recycled as the Exorcists chapter of Space Marines), the Star Child (a Warp entity that supposedly represents the Emperor's soul, today laughed off as a delusion of the Eldar) and the Sensei (supposedly the "sons" or descendants of the Emperor).
7th edition ended up reversing much of the sufferers of Chuck Cunningham Syndrome, by bringing back some elements of the fluff that was largely forgotten. The most prominent of these are the return of the Imperial Knights and the Kastellan Combat Automata, the former of which was quietly dropped in the latest (and last) edition of Epic 40k and the latter hasn't even been mentioned since 3rd edition of normal 40k.
The Warlord titan got a lot of flak during it's teaser for looking too much like "an Imperial Knight on steroids". Many old beards were quick to point out that it was in fact based on the first Warlord Titan model released for Epic 40k, which many people have long since forgotten even existed due to the ubiquity of the "Lucius" pattern warlord everyone's so used to now.
The loss of squats and Eldar exodites was not because they were too silly, but because 40k was distancing itself from its roots as simply Warhammer IN SPACE!! Squats were obviously just space dwarfs while exodites were wood elves, and neither really had a place in the game or lore other than as ersatz versions of their fantasy counterparts.
Despite being featured in a couple of cards when the Gravekeeper theme first kicked off in the Yu-Gi-Oh! TCG, Cobraman Sakuzy and any references to him completely vanished in later expansions, most likely due to not being useful at all in any deck and being an ill-fit for the theme.