In my opinion, yes, I would wash the muslin. Since you are using it as a separator, not in a quilt. There may be a finish on it that in the long run will not be nice to older fabrics. You might want to try a commercial laundry with a large washer and just do the entire bolt. But I also am not certain you really need to separate them. I would just stack them on top of each other and place an overall dust catcher bedspread on top.