Stress can contribute to RI too, so I'd leave her be. Maybe only handle once a week for a few minutes for now. BP's don't need to be handled often to "keep them tame", they naturally are!
I wouldn't even think about climbing for muscle tone, that she's stressed and refusing food. Having muscle tone is great, if the BP is healthy. If the BP is not totally healthy or having other issues, climbing/taking them out to handle is low priority... they don't "need" it to survive. Make sure her warm side temps are on point, and her enclosure is clean with good ventilation, and let her be.
As a general rule, if a BP is refusing food due to potential stress or illness (and not just doing a fast), you should minimize handling/don't handle at all until they eat.
I also agree that if the vet didn't do a culture for her last RI, it's possible she never fully recovered from it. There are different types of RI, and you won't know what medications to use for sure until a culture has been done.
ETA: I know there are people who put SO MUCH emphasis on "exercise, enrichment, muscle tone" that it seems to actually mislead some owners to believe that it is critical for keeping a ball python healthy and sickness-free. It is not. It's more like icing on the cake, once the snake is already healthy. If the snake is sick/stressed, don't even think about it... worry about the basics first (temps, humidity, hiding spots, minimal handling). Forcing exercise outside the enclosure is simply additional stress.