Here's some advice from a sailing forum

www.sailnet.com/forums/gear-maintenance-articles/19829-sail-care-cleaning.html

Mildew Prevention is the best tactic, but if mildew has attacked the sail, treat it immediately and isolate the area from the rest of the sail to prevent spreading. Do not use bleach on Kevlar or nylon. All other laminates and coatings can take a weak chlorine bleach solution of one percent or less. Most bleach (sodium hypochlorite) solutions off the shelf, like Clorox, are a 5.25 percent solution and will need to be diluted. Some commercial brands of mildew cleaners like Tilex have three percent or less solution of bleach and can be used with dilution and a litte extra care. Lysol is a fungicide that when sprayed on the sail will kill existing spores and inhibit any additional growth. After the organism is killed, most of the stain can be removed by soaking (not scrubbing) in a fungicide for 12 or more hours. Always rinse thoroughly to ensure there is no bleach residue left on the sail.

It is possible to soak and clean a sail in a swimming pool, but this should only be done to polyester sails when you are sure that the chlorine or other chemical level of the water is within the tolerance level of the coating. Never place a Kevlar or nylon sail in the pool.

Another one
www.doityourself.com/stry/qnacleaning8

Q. I have mold on a nylon kayak spray skirt. How can I remove the mold?

A. Mold and mildew stains on fabric tend to be next to impossible to remove. At best, you can expect to lighten them. You may have some success blotting stains with lemon juice and sprinkling on some salt and place in the sun. An enzyme digester cleaner may also provide you with some success.

Hmm I always thought a mild soap solution would do the trick too.

Lara, I've had great success with an oxy acetylene torch.

Might be worth giving homebrew sanitizer a shot.