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.
Depending on the design, the heating coil may have collapsed and is shorting out at various points
This may cause it to run hotter than intended, and result in problems you describe
Measure the current with a meter and compare to manufacturers label, if much higher it's time to scrap it. Unlikely to be easily repairable if it has a heating coil
If it is running hot it is likely to fail soon and not heat at all
Modern crock-pots used solid elements, not coils. They also often have physical temperature regulation systems, not just a simple element selector switch
Best Answer
The USUAL problem with "warm" (or off/unplugged) on a crockpot is when food that is not hot is placed in one and left on those settings, where it does not quickly warm to a safe temperature range.
If the food was on "High" for 2 hours, it was hot. Depending on the specifics of the "warm" setting on your crockpot, it's somewhere between no risk (warm is 140F or above, maintaining a safe serving temperature) or low risk if for some bizzare reason they set it lower (food would still take a long time to cool below 140 °F, and thus would not actually have been below that temperature for anywhere near the full 45 minutes.)
I honestly can't imagine that a manufacturer would have chosen the second (unsafe) option, but I don't know for sure what your specific model actually does.