Frankly speaking, I would just let them fade over time. It's really tough with something that old, where you have no idea what was used to make the marks. Most everything I can think of to try is either unlikely to work or likely to damage the fabric.
Is she sure the embroidery thread won't bleed down the line? A lot of embroidery thread is not colorfast. This might be the rare quilt that needs to be dry-cleaned just in case.....