Use Unions to subtract part, then add bones

Is there a way to make it so when you subtract a mesh part that has bones, the bones will not work any more. Is there a way to get around this?

Have you tried updating the bones? like re-assigning them to meshes?

Roblox documentation states that SubtractAsync creates new mesh;

GeometryService | Documentation - Roblox Creator Hub
Creates one or more PartOperations or MeshParts from one part minus the space occupied by other parts.

Yea I have, it just seems to bug out due to the new shape of the Mesh, I may be doing it wrong