Answer based on context:

The command of this expedition would be entrusted to Miguel de Noronha, 4th Count of Linhares, for which he was appointed Capitán General del Mar Océano, but he eventually declined to lead the fleet as he did not trust in the success of the expedition. García Álvarez de Toledo, 6th Marquis of Villafranca also rejected its command, but not the Count of Torre, Dom Fernando de Mascarenhas, former Portuguese governor of Tangier. The same day that the French siege of Hondarribia was lifted, he was given the command of 41 ships, of which 23 were Portuguese and were commanded by Admiral Dom Francisco Melo de Castro and Vice Adm. Dom Cosme Couto de Barbosa, and 18 were Castilian under Admiral Juan de la Vega y Bazán and Vice Adm. Francisco Díaz de Pimienta. 5,000 soldiers of infantry were embarked aboard this ships. Half of them were of the Tercio de Anfibios, a unit specialized in the naval fighting. The fleet stopped at the islands of Cape Verde, where an epidemic struck the crews of the ships, resulting in the death of 3,000 men and a number plus larger of incapacitated at the arrival of the fleet to Salvador da Bahia. Mascarenhas, ignoring his orders for an immediate assault upon Recife, spent about a year in the town before set sail again, which was done in January 1640 with the intention of land 1,200 soldiers under Luís Barbalho Bezerra to reinforce the Portuguese guerrilla surrounding the Dutch garrison of Pernambuco.

What happened second: siege of Hondarribia was lifted or epidemic struck the crews?
epidemic struck the crews