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.
Unfortunately you cannot apply the scale of linked from another file objects. The reason this is so is because it is an exact copy from the original file and so you cannot change many parameters