The correct answer to this open question is the following.
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According to the King, what happened to Francisco Pereira Coutinho, was that Pereira had a shipwreck and was captured by Native Indians in Itaparica, Brazil. The Indians killed him.
Let's remember that King Jhon III bestowed the region known as Bahía de Todos los Santos(Bay of All Saints) to Francisco Pereira Coutinho, in March 1534.
Pereira traveled to this place in 1936 and built homes there, a fortress, and a castle. The problem was that he was despotic, arrogant, and cruel to the Native Indians.