When China needs to do it, they also have major brainwashing power. Just look at Xinjiang going from literal ISIS town into likely one of the most vocally pro Chinese areas in less than a decade.
Separatists on Taiwan are majorly screwed whichever way one lays it up. Because Beijing has fully separated it's economy from Taiwan, frankly speaking they can reduce the whole province to a wasteland without affecting the 30 trillion $ economy of the mainland.
The current leadership has made pledges to do negotiation with the anti government leaders. This is a common solution in many civil conflicts internationally. But if they fail, they will either have to change the method or be replaced by a different leadership.
Because Taiwan does not contribute to the national economy at all, even a solution where the future of the province is an Israel like landscape of perpetually bombed and starved masses of separatists interspersed with dots of settlements populated by mainland imported people, the net effect to China's national security and economy will be positive, not negative.
