I have two cushions, and one of the cushions is an instance of another(object data synchronized). So I wanted to unwrap the cushion, but it came out odd because the scale is wrong.So I am wondering: How to apply the scale to this object which is an instance of another one?(basically to a multi-user object)
You can't apply scale on multi-user object data. You will have to make the single user objects. U > Single User
You can relink the object data after applying the scale. See this answer for more information on relinking.