I understand that an autopsy may sometimes be performed if doing so is useful to gain knowledge that may be used to prevent deadly diseases or sicknesses in other people. Refer to this M.Y. answer.
May someone do an autopsy on his own father, or is there an extra prohibition of kibbud av that may prevent him / her from doing so? What if he is the expert or only person who has ample knowledge in the sickness that he is researching?
Dr. Jonathan Rosman in the Journal of Halacha (here, p. 42) brings a gemara in Baba Batra 154a as a source that a family has a special obligation not to desecrate a body
The Gemara in Bava Batra discusses a case where a father dies and leaves property to his son. The son immediately sells the property and soon after dies as well. The son’s inheritors claim that the deceased had not reached adulthood and therefore the sale should be void and the property should belong to the father’s other heirs. The buyers claim that the deceased had reached adulthood, thus the sale is legally binding and the property therefore belongs to them. Rabbi Akiva was asked whether it would be permitted to exhume the body to see if the deceased had physical signs of adulthood.
Rabbi Akiva answered that the body should not be examined because of nivul hamet, or desecration of the dead. Rabbi Akiva further added that after death signs of puberty change and are unreliable in determining adulthood, and therefore examining the body would not be helpful.
Tosafot state that Rabbi Akiva was compelled to provide both answers because there are cases where it would have been permissible to examine the body. Tosafot write that the buyers have the right to examine the body since they stand to lose money. Financial loss is a permissible reason to examine the body, according to Tosafot. However, suggest Tosafot, the family has a special obligation to the deceased and thus even for financial loss cannot degrade the body. Therefore, Rabbi Akiva had to bring the second answer that even for the buyers who are permitted to defile the body because of financial loss, examining the body would not help because signs of puberty change after death. According to Tosafot, the prohibition of nivul hamet applies only when there is no good reason to defile the deceased; but for an acceptable purpose, such as monetary loss, nivul hamet would not apply.
Although you are correct that a doctor son can treat his father if he is the only one (or the best one) to do so (MT Hilkhot Mamrim 5:7 or here on MY), in the context of an autopsy it is difficult to imagine one couldn't bring a second specialist since there is less urgency.
