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The Arabs had significant influence in Southeast Asia, and were all over the Philippines, yes. However, the whole nation was not Islamic, in fact, by the time the Spanish came, there were some areas of the Philippines which were still Pagan (Either Hindu or Animist) and warred with Muslims still.
Also, Arab-Islamic colonization in the Philippines wasn't only economic it was also imperialistic. The Sultanate of Brunei in Borneo, for example, had once invaded the Kingdom of Tondo in Luzon island and supplanted it with their vassal-state, the Kingdom of Manila. Brunei's Sultan also married Sulu's princess, Leila Mecana, to expand their territory even unto the Sulu archipelago.
There are also other examples, like, the Kedatuan of Dapitan in Bohol island which was utterly destroyed by the Papuan-speaking Sultanate of Ternate and had to re-establish their Kedatuan in Northern Mindanao, before they sided with the Spanish to attack their Muslim neighbors.
The Rajahs of Cebu and Butuan also had their fair-share of slave-raiding and warfare from the Sultanate of Maguindanao.
As you can see, the whole Philippines wasn't Muslim then, but were rapidly being islamized before the Spanish came and allied with the Non-Muslim states and Christianized the whole lot of us.
And why are you crying over the Christians attacking and converting Muslim lands when Muslims have been doing that far longer and more extensively. Muslims invaded over 2/3rds of the former Christian Roman Empire by annexing the Middle East, North Africa and Iberia, yet when Spaniards and Iberians Rechristianize Islamic Spain and Christianize Islamic Philippines, you throw a hissy fit.
The Spanish had a particular hate against the Arab-Muslims considering that their homeland was invaded by Muslims and it took 750 years of war before the last Islamic Emirate in Iberia, the Emirate of Granada, was destroyed by the expanding Christian Kingdoms, lead by the Kingdom of Castille.
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