A. I should add that if you changed foods recently, it is possible he could have a food allergy as well. Otherwise, it sounds as though he has a tender spot. Work on counter conditioning (happy tone of voice and treats to replace the fear of paws touched) and desensitizing (repetition of treats and gentle paw touching) him.
A. It is possible a nail was trimmed a bit too close to the quick. If he is licking the bottom of his paw, perhaps he scraped it on a rough surface (a rock for example) running. Lastly, if he were to be licking both paws, he could have an environmental allergy. To get him comfortable with touching his paws, you will need to move slowly and gently pairing touch with lots of tasty treats. Do not force too much on him too soon. The goal is to teach him that touching paws equals positive things. Start by touching and petting other parts of his body eventually moving to his leg (treat at this point) and down to his paws (lots of tasty treats!). It may take several days to gain his trust but eventually he should become more comfortable.
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