Probably not, but blatantly violating the sovereignty of the Philippines in order to keep these bases operating against the will of the host country would be potentially devastating to the US' position internationally. It's been a long held position of the US that their bases are there at the consent of the host country. Outside of controversial exceptions like Guantanamo, If allies like Italy wanted the US out of Aviano Air Base, they're out. Reneging on that policy has the possibility to drive deep rifts between the US and its allies.

It'll be up to the the decision makers upstairs if using those bases to defend Taiwan is worth risking a major hit to the country's relations with its allies if it pursued such a course of action.