The state order kidnapping of young Jewish children (boys) in 1493 under king Joao II, their separation from parents (as punishment for not paying the debt for entering Portugal after expulsion from Casitlle), forceful conversion to Christianity and subsequent sending to island of Sao Tome - a tropical, disease ridden island where many soon died - was a horrible tragedy, which we can say fortunately was a one-off thing.

Not that the Portuguese took much pity or compassion for the jews. Manuel's policy towards Jews was only slightly more conciliatory on the account of their economic importance, and still in 1497, due to this being a condition of his marriage to spanish princess, he order expulsion and then forced mass conversion of Jews in Portugal (to prevent them from leaving). In the subsequent decades, position of this New Christians was worsening and never at ease nor was their status equal to the old christians. Yet they managed to somewhat integrate in (and perhaps even dominate) the economic life of Portugal. Inquisition was formally set up in Portugal in 1539, and effectively started operating in 1544/1545 when first public burnings took place.

The increasing pressure in mainland Portugal, and their commercial deals, lead many prominent New Christians to move to Portuguese colonies, some to India, some to Brazil whose colonization has picked up pace in the second half of the 16th century. Brazil's main industry was plantation-style cultivation of sugar, which needed many slaves, and New Christians became involved in slave trade and reached Africa and Angola specifically which was the main exporter of slaves to Brazil. The increased presence of New Christians in colonies made the Portuguese Crown and Church uneasy, and not only were they not forcibly sending, there were intermittent official bans on New Christians moving to colonies. Still there was many ways which one could circumvent or bribe it's way into colonies and many did exactly that.

Angola was settled after 1569, by a donatoria grant to a old christian Paolo Dias de Novais in 1571, where he was awarded hereditary control, lot's of judicial and administrative rights, parts of royal taxes in the new area, and pretty much non-interference from the crown - on the account that he does this all out of his pocket, and not commit treason or other serious crimes. In this form the settlement began, construction of first forts and towns (Luanda) and skirmishing wars with Angolan native population. From the documents we have we don't really see any New Christian forced settlement, nor would the King have this power ( they would be contradicting the grant). There could have been a New Christian voluntary involvement, as they were known as financiers, but we don't have any evidence to support it. It is also unlikely as Angola was picked as Jesuits to conduct their missionary activities in Africa, which they conducted extensively. While Jesuits weren't Dominicans who were leading the Inquisition, they would probably not really tolerate a significant New Christian population.

Still, New Christian involvement in Angola is documented, especially in the 17th century, mostly in the slave trade connection for the Brazilian Bahia where many New Christians had plantation and sugar mills. Inquisitions high activitiy in the 1630s and Dutch-Portuguese war in the 1640s and 1650s where parts of Brazil and Angola changed hands (first to Dutch then back to Portuguese) affected New Christian presence, as it seems they withdrew from the area with the Dutch. But this is a time period I am really not that familiar with.

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You can read more about the events surrounding Sao Tome children:

F. Soyer: The Persecution of the Jews and Muslims of Portugal: King Manuel I and the End of Religious Tolerance (1496–7) pages 130-132

And about Angola settlement

M. Newitt - The Portuguese in West Africa, 1415–1670: A Documentary History pages 121-148

A.R.Disney - A History of Portugal and the Portuguese Empire: From Beginnings to 1807 - Volume II (2009) pages 70-84