When someone is in the flesh, they're somewhere in-person. A face-to-face meeting happens in the flesh.
Your flesh is your skin, and the word flesh is often used as shorthand for people's entire bodies. Along those lines, we say someone is in the flesh when they are physically present somewhere. If you went to the Grand Canyon, you were there in the flesh. If you go to a restaurant with someone, you saw them in the flesh. Talking on the phone or emailing are not examples of communicating in the flesh, which requires being present.