This is a really interesting question, and there are a lot of different ways to look at it. There are definitely crops that have gone extinct because of overuse, there are food cultures that have mostly died out or faded into obscurity over time as newer and "better" foods became available, and there are food cultures that have been harmed even recently by racist and xenophobic policies that have limited food access for certain groups. Since this is the rare question that allows me to talk about both of my scholarly interests in Ancient Rome and in the United States, I'm going to address some examples from both that will hopefully give you an idea of why, how, and when some foods have "died out." With the exception of species extinction, though, I think it's also important to realize that there are a lot of culinary historians, community activists, anthropologists and cooks who work to help revitalize culinary traditions, resurrect or reintroduce certain subspecies of plants (like corn and potatoes), so something might have disappeared for now, but tastes and foodways are always changing.

Starting with the most cut-and-dry case of species extinction I'm aware of, the plant Silphium was so widely used by the ancient greeks and romans for cooking, medicinal purposes, livestock feed, etc, that it became extinct. Pliny the Elder's Natural Histories recounts its many uses, and it appears in Apicius' recipes. the article Pliny the Elder's Silphium: First Recorded Species Extinction concludes that since we can't positively identify the plant, we can't totally know if it's extinct, but it's certainly no longer a part of our culinary consciousness in anyway. It's possible that overgrazing or over-harvesting eventually killed the plant off, but at its height, it was a commonly used spice, a way to give livestock who grazed on and ate it a special flavor. And now it's gone. But this kind of species extinction is comparatively rare (though we've eaten a fair few animals into extinction, there's a sort or trade book called Lost Feast: Culinary Extinction and the Future of Food that deals more extensively with the topic) when you think about the 'history' of lost food.

Ancient Rome provides us with several other helpful examples of lost food, especially considering Roman food itself has almost totally "died out," and contemporary Italian food uses a bunch of different foods that didn't even exist in Ancient Rome. One of the staple condiments of ancient Rome (which people love to compare to Ketchup) was a fermented fish sauce known as Garum. A lot of contemporary readers who encounter depictions of Garum and its production (placing a sealed jar of fish and salt in the hot sun for a few weeks, and stirred occasionally) react with some kind of disgust (source: any student who have ever taken Latin has probably encountered this), even though it's not actually that dissimilar to fish sauces used in East Asian cooking. But it's so unfamiliar to western audiences because it has fallen so far out of fashion that it sound unappealing. This is broadly tru of lots of Roman cooking. Most people don't want to chow down on a fest of Lamprey Eel and dormice or a boar stuffed with living birds, which are represented as kind of extreme versions of what the rich ate (in Petronius' Satyricon). Some of the staples of Italian food: tomato, corn, potato, eggplant, spinach, citrus-- just weren't very common in ancient Rome. There was honey, but not sugar. Spices and herbs were different. Ancient artichokes were very very different than the ones we eat now, which mostly date back to the middle ages. Food and tastes changed and evolved over time, and access to 'new world' foods significantly changed the mediterranean diet. Roman food was, comparatively, outdated, and mostly exists now among classicists and hobbyists.

When thinking about the food of pre- Columbia America, it's important to understand that the food and crops we eat today are often very different than even the same varieties of crops cultivated in the past. The difference isn't always night and day, but the corn you eat on the table has been cultivated for taste and sweetness and is a different product than the corn in ancient indigenous foodways. Many indigenous heritage corn varieties were lost during the forced eviction of Native American tribes to Oklahoma. Post-industrial foodways are different than ancient and indigenous foodways in so many different ways, and the theft of indigenous land and forced removal of Native Americans onto reservations irreparable damaged, for example, the culinary practices and foodways of Native American communities, because native American foodways are so location specific and vary so greatly from tribe to tribe. I am, admittedly, not super well versed in Native American food histories, but there's a book called Decolonizing the Diet: Nutrition, Immunity, and the Warning from Early America, that explores the impacts of settle colonialism and industrialization on Native American culinary practices.

This last example might seem like a bit of a stretch, but I think there's also a case to made that redlining policies, the lack of fresh food in many predominately Black and Brown neighborhoods (Food Deserts), discriminatory loan practices by the USDA, centuries of nutrient depletion in southern land from cash crop farming, the medicalization of southern and soul food, have also fundamentally changed southern and soul foodways. While these practices haven't erased the idea of soul food, they've changed and corrupted it by all but removing Black Americans from the food system (who make up 5% of farmers)and reducing access to fresh food in predominately Black communities, which has created the stereotype of southern food and soul food as lacking fresh vegetables, being all fried and unhealthy, even though that's not what the history of soul food shows us. This is also changing, and there are lots of chefs and historians (Michael Twitty, Adrian Miller) who are emphasizing traditional southern foodways and talking about the ways that institutionalized racism has eliminated access to traditional foods from some communities.

This is really only the tip of the iceberg, but I think it's a decent representation of how foodways can disappear, or otherwise change. I'd welcome additions from non-western historians too!