I suspect "warm" is meant to maintain temperature, rather than raise it. My crock pots are too ancient to have anything other than "high" and "low", so I can't assert any real authority. However, if you reach 145F within the first hour at the highest setting, then keep it at "warm", and test the temperature after about 30 minutes with an instant-read thermometer and it stays around 140-160F, you'll probably be fine. Personally, I'd test the temperature first by cooking water.
If the temperature stays above 140F at low, the worst risk you'll have is overcooking. Beans and vegetables like carrots and celery can overcook fairly easily in a crock pot, but higher collagen meats meant for stews tend to be fine when cooked for extended periods. Most crock pot recipes for stews and soups usually hold fine when at low for a full workday, although that's presuming a somewhat 70s-era soup aesthetic, which is probable for a crockpot recipe.
However, I would be inclined to attempt the recipe using the low setting rather than reducing it to warm, if you're not going to test the temperature first. If it turns out to be overcooked, you can always puree the ingredients with a blender...
I also doubt that switching to "warm" would be dramatically less likely to overcook the food than "low", unless it holds at a pretty stable 140F, and low ends up somewhere around 160F.
From experience cooking chili in Crock-Pot brand slow cookers, each time you change the setting (at least from high to low or vice versa), it resets the timer. Also, of course, so does high->off->high.
So, (at least my Crock-Pots) would cook on low until midnight in your example.
Well, unless the power went out for three seconds. (It'd be off after the power blip.)
Personally, I've switched to non-"programmable" slow cookers.
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At best, you'll have toasted beans. At worst they will be burnt. I'm guessing these are dried or otherwise you wouldn't worry. Curious what you find out.