So, according to Readings in Philippine History by Horacio de la Costa, the early 17th century was a dire time for the Spanish East Indies. The Dutch East India Company's economic warfare, combined with Moro raids in the Visayas, had driven the Spaniards to Manila alone. Many feared that the whole colony would be taken, with the blockades of the Dutchmen almost bringing down the Manila trade, and thus the whole colony, to its knees.
However, the Spaniards fought back, the Governor General of the time, Juan de Silva, leading a naval battle against the Dutchmen at Playa Honda in 1610 and driving them back.
And then he took the offensive, leading a large expedition south to rendezvous with the Portuguese at Malacca and drive out the Dutchmen.
However, the Portuguese never came, defeated at the Moluccas, and Juan de Silva himself died of dysentery. The Dutch gave no battle and instead allied with the sultanates to crush the Spanish bases which had been stripped of material to supply the battle.
Never again were the Spaniards able to put together such a large fleet, and thus the Spanish East Indies were restricted to Luzon and the Visayas until the 19th century, and never again extended south of Mindanao. The presence of Dutchmen in Malacca became permanent, and the Eighty Years' War in Asia became a defensive one.
So, with all this in mind, what if Juan de Silva instead sails to the Moluccas just as the Portuguese were attacked by the Dutchmen, and crushes them in a decisive battle?