It might be that the small rat pup is all being used up, especially if it's too small, you will see swelling around the cloaca often known as sausage but. normally a good long soak in warmish water will help solve the problem,
Does the small rat pup leave a bulge at all when fed?
It should only be slightly anyway. the prey item as a rule of thumb I use is a mouse or rat should either be the same size or slightly bigger than the fattest part of your snakes body
Remember sonoran are a smaller boa anyway
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