Not to derail this thread, but what extinct races do we have confirmed information about? Lizardmen are in Mind Lords and the pixies are mentioned in the 3e supplement material this site has. Are gnomes mentioned in the 3e material anywhere?
As for my own suggestion I tend to go in one of three directions when using gnomes.
1) Earth Spirits: Basically gnomes are elemental beings that take a large deal of inspiration from svirneblin while also having inherent affinity for the underground. These gnomes are often on the higher end of the tech scale of my settings when I use them. Giving them a limited tremor sense so that other races think they have a magical sense of precognition is a fun approach, an even more potent equivalent to dwarven stone cunning could be warranted, as well as a penalty for when the gnome isn’t touching stone or soil (they would hate sailing, climbing trees, etc.)
2) Fair Folk: Pathfinder covered this approach rather thoroughly, but gnomes are a good way of having a fae critter in your setting if you’re not using elves for that or you want a “wee folk” type of fae race. This sort of gnome is the kind that’s the most magical and are often among the longer lived races of the setting when I use this type of gnome. Considering fae would be remarkably rare in Athas, this is the other angle that’d work easily for dark sun gnomes going extinct. It does however step close towards the lore we have about pixies being forest spirits, but it could still work.
3) Craftsmen: While I think Tinker Gnomes are garbage I have used gnomes as the magical craftsmen of the setting on more than one occasion, particularly if my setting doesn’t allow dwarves to use arcane magic.This is what gnomes were originally for back in old school D&D and there’s ways to fit this schtick in depending on your setting. For Dark Sun this angle is tricky due to arcane magic not being much of a thing (edit: when the gnomes would’ve been around at least). However you could take a page out of the elves’ book and depict gnomes as one of the other races that was taking well to learning preserving and defiling magic. Perhaps they crafted a bunch of fantastical psionic items and once they started dabbling with magic as well they raised enough of a concern among the Champions that they came down hard on the gnomes to make sure no one would rival their supremacy. Imagine ancient gnome ruins with hybrid relics of psionic and magical power…