Will taking doxycycline hyclate for 3 days put me at risk of getting c-diff how high is the risk?

This would be little or no risk. But this is a peculiar treatment. When doxycycline is needed, almost always treatment is for at least a week. The most common reason for doxycycline is chlamydia or nongonococcal urethritis (NGU). These require 7 days treatment.

Risk is minimal with doxycycline. You can further minimize the risk by taking a daily probiotic.