Pinto beans have slightly lower calories compared to navy beans. While pinto beans contain sodium, the navy beans do not have sodium. I think the two can be substituted for each other. Consult a nutritionist for more information.
Absolutely they can be swapped for each other in recipes. Pinto beans are a bit harder and have more fiber.....so if you are planning to use the DRY beans----pintos will need to be soaked about 2-3 hours longer than navy beans.