Rust stains need acid-based removal, and can eat through the cotton. Most old stains can be taken out with prolonged soaking - days, not hours. A combination of enzyme cleaner and gentle detergent usually works. For antique quilts, I put in laundry basket or milk crate in bathtub, never directly in a washer. Pulling a wet quilt up and out can do some serious damage.
Cross stitch is usually done in cotton or silk thread. On a bed quilt, animal claws can get tangled easily and rip out stitches and fabric.