Some people are confused about Twinrova. How is it that you defeat Twinrova in OoT, then Koume and Kotake are good witches in MM, and then they are bad again in Oracle? The answer to this question is quite simple, if you are well-informed of the facts.
First of all, some facts about Koume and Kotake. They are called the "Sorceress Sisters Twinrova," and are too old Gerudo witches. They are called by the name of Koume and Kotake, Twinrova Koume and Twinrova Kotake, or simply Twinrova. Navi tells Link in OoT that they are "Ganondorf's surrogate mother." When Link defeats Twinrova, they are "only" 400 years old. Before they disappear, Twinrova tells Link, "I'll come back to haunt you!"
These facts tell us that these Gerudo witches have very long lifespans. They are twins, but can combine into one. At different times they are referred to as being one entity, Twinrova (possible the form they take when they perform their "Double Dynamite Attack."
The next time we see Koume and Kotake is in Majora's Mask. Remember that this takes place in Termina, a parallel world. Everything in Termina is similar to Hyrule, including the land and the people. But the same people do not appear in both Hyrule and Termina. The Koume and Kotake in Termina are doubles of Twinrova in Hyrule. Because their history and upbringing is different, the Terminan Koume and Kotake use their sorceress powers for good instead of evil.
Now, since Twinrova was the surrogate mother of Ganondorf, has a long lifespan, and vows to haunt Link after she dies, you see the precedent for her appearance in the Oracle games. She must have been planning for her death in OoT; otherwise she wouldn't boast that she would come back to haunt Link. It is unclear when exactly Twinrova revived herself after OoT (or if she required reviving at all), but the Oracle games hint that Twinrova has been around for a long time before the events in the game. Both Maku Trees seem to know about Twinrova already, which means Twinrova has already been around for a while.
Table of Contents: