Those islands are already KMT aligned, and the populations have strong cultural and familial ties to the mainland. It is very doubtful they would be targets in the event of AR.Time to put the proposals of build bridges directly connecting Kinmen Islands with Xiamen, and Matsu Islands with Fuzhou back on the table.
In case of war between the PRC and Taiwan separatist forces, the Kinmen and Matsu Islands would never last under fierce PLA bombardment. Any resistance attempt on those islands are certain to be futile anyways.
If those bridges are built and PLAGF tanks suddenly rolled over those bridges and land on the islands (with or without launching AR against Taiwan itself), then so be it.
However, strict immigration and custom checks should be enacted at the border crossings between Kinmen and Matsu Islands with mainland China to stem and prevent infiltrations of Taiwan-based separatist agents and alphabet soup organizations' personnel into mainland China, alongside dangerous goods and items which these agents and personnel would bring.
China doesn't need the islands to take Taiwan. They hold little to no strategic value, and are in fact counter-productive to attack/occupy at the expense of antagonising the locals and the KMT by extension.
If the PLA were to attack, they'd go for Taiwan proper, directly.