The two ways of relating what a person has said are 1)direct and 2)indirect (reported speech).In direct speech, the original speaker's exact words are repeated. In indirect/reported speech, the exact meaning is expressed but not necessarily using the original speaker's exact words. Pronouns and possessive adjectives usually change from first or second person to the third person except when the speaker is reporting his own words. Sometimes a noun can be inserted to avoid doubt.
When we turn direct questions and exclamations into indirect speech, they are converted to affirmative statement .( ? and ! is not used).
Option D is correct as when we convert the given direct question to indirect speech which doesn't start with a question word, then if/whether is used, the present perfect tense is changed to past perfect tense (had) and you is changed to I. Also, as Any answers positively (yes), the dialogue are connected using to which and the present perfect tense is changed to past perfect tense.
The other options are wrong as have, you, and have can't be used.
The correct answer is D)Amy asked if I had to leave early to which I replied in affirmation and said that I had some work.