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Assume that the father is a Gentile who married a Jewish woman. The child, who is Jewish, obviously, becomes a mohel.
Years, later, the father decides to convert, so he needs a brit. Is the son allowed to the brit on his father, or is this in conflict with any halacha that states that a child is not allowed to physically "injure" his father?
You can ask the same question about a Jewish-from-birth father who happened never to have been circumcised. Minchas Chinuch 48 rules that the sin of injuring one's parent does not apply if one does it with the parent's permission. Shulchan Aruch YD 241:3 seems to disagree, but Rama clarifies that SA is strict only if no one else is available to do what the father needs done. The case of a convert father that you described would seem to be included by rabbinical decree (SA :9, q.v.).
So in short it would seem another circumciser would be preferred according to SA but that it is permitted if another circumciser isn't available; and Minchas Chinuch permits it anyway.
