The so-called emphatic do has many uses in English.
To add emphasis to an entire sentence: "He does like spinach. He really does!"
To add emphasis to an imperative: "Do come in." (actually softens the command)
To add emphasis to a frequency adverb: "He never did understand his father." "She always does manage to hurt her mother's feelings."
To contradict a negative statement: "You didn't do your homework, did you?" "Oh, but I did finish it."
To ask a clarifying question about a previous negative statement: "Ridwell didn't take the tools." "Then who did take the tools?"
To indicate a strong concession: "Although the Clintons denied any wrong-doing, they did return some of the gifts."