|What gets destroyed by cooking is vitamins. If vegetables are cooked in water, some of the vitamins and minerals will be lost to the water but if the water is retained in what you are cooking (as in soup) then they are not lost, only if the cooking water is discarded.|
Don't worry about losing nutrients in chili by cooking. Most of what you have in chili (meat and beans) are primarily sources of protein, carbohydrates, and fiber. You're not talking about a lot of vitamins here. Whatever minerals are present are going to be retained.
The primary concern over cooking times is vitamins, which will break down with extended cooking. This is why steaming or stir-frying vegetables briefly is considered better than boiling or cooking over a period of time. The shorter cooking time and less (if any) water retains the vitamins. The longer they are cooked, the more vitamins will be lost.
You want to understand what the primary advantage of each food is and what is retained or lost when cooking. Protein, carbs, and fiber will not be lost. Minerals will be leached out to a certain extent in water but will not be destroyed by heat. Vitamins will be leached out in water and will be lost with extended cooking, but this is more of a concern when, say, you are cooking broccoli, a very good source of vitamins, and is less of a problem when, say, you are cooking potatoes, not a big source of vitamins.
Don't worry about the chili. Cook it as long as you want.
I was raised on a lot of mushy cooked forever foods, including gray split pea soup and stews a toothless dog wouldnt eat.
That's the cook's fault and not the cooking time. I have a delicious recipe for split pea soup. Of course, it's the smoked ham hocks that make it fabulous! Split peas *should* be cooked a long time and will actually be more palatable and digestible. But they need to be seasoned well. That's the trick.