I’ve been reading Victor Perera’s “The Cross and the Pear Tree”, a riveting read about his long search tracing back the history of his family and their namesake’s expulsion from Portugal from the mid sixteenth century to the early nineteenth.
Also stumbled on to a page of resources at SephardicGen, and a page archived on the Wayback Machine, listing the family names from the Inquisition Archives in the Torre do Tombo. And Xavier is included. The page sites as it source a book “Raizes Judaicas No Brasil – O Arquivo Secreto da Inquisicao” by Flavio Mendes Carvalho.
Xavier is not a name included in a very long list of sephardic names.
Other links at Sephardim.