The person's flesh, or physical body, is a metonym for the person. Alternate translation: "not physically present with you" (See: [[rc://en/ta/man/jit/figs-metonymy]])
Being with someone in spirit is a metaphor for thinking continually about that person. Alternate translation: "I continually think about you" (See: [[rc://en/ta/man/jit/figs-idiom]])