I think there are some products to clean up old linens. Grandma's spot remover and the Carbona line come to mind. I think you can get those at JoAnns and maybe other fabric stores. And How about Oxyclean. I soak my husbands work shirts in oxyclean for up to a week without damaging the embroidered logo. Here is a link I found for vintage linen stains.
http://reviews.ebay.com/Linda-apos-s...00000000014562
I googled 'cleaning vintage embroidery stains'
Hope you find something!