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Mold and funguses are best removed by using 'caustics' which dissolve the cells. Chlorine, clorox, vinegar only kills/stuns these cells and leaves these cells to become the nutrient sources for future species of fungal microorganisms. Lye soap, lye, or 'strong' alkaline soaps and detergents including TriSodiumPhosphate-TSP or sodium silicate based detergents are 'dissolvers' of fungal cells.
Funguses spread by the release into the atmosphere their spores; dead or removed funguses generate no spores.

Mechanically you have to 'scrub' more than visible surfaces; you must remove all the growing fungals from all the 'hidden' spaces: under the sole, under the 'pan liner', bilge, the WATER TANK VENT HOSE, etc.
Once all the interior spaces are 'thoroughly cleaned', then consider to 'spritz' (not on painted or varnished surfaces) one of the sodium silicate detergents (Roll-ON™ or Tuff-eNuff™) or 3M Marine Mildew Block (16.9 fl-Ounce) : Amazon.com : [email protected]@[email protected]@http://ecx.images-amazon.com/images/I/[email protected]@[email protected]@31PswfXL5OL ... and simply let dry - dont wipe off !!!! This will be a modern equivalent of 'white-washing' - a sure-fire method of mold/mildew prevention discovered by our far distant ancestors - caustics !!!, which deactivates mold/mildew/fungal spores !!!!!!! .... and no matter what the internal 'humidity or air-flow' inside your boat.

If you are sensitive and/or reactive to molds/mildews/funguses, be SURE to wear a RESPIRATOR, goggles, etc. when cleaning. NEVER EVER 'clean' mold/mildew/fungus when it's 'dry' as you will only release and spread the spores into the atmosphere; before cleaning always wet it down (water, clorox, sodium silicate, etc.) to prevent/lessen the spread of the SPORES and prevent you from aspirating them deeply into your lungs --- advice for even 'healthy' folks.

If your 'sensitivity' to mold, etc. is high, consider to hire a 'dairyman' or someone from a 'dairy maintenance' company to do the bulk of the cleaning and disinfection for you (but dont allow them to 'treat' any painted or varnished surfaces - you do this as for sure theyre going to be using 'strong caustics'.).

For long term storage/closure of your boat, consider to use "Para-formaldehyde" crystals .... put a measure of crystals in a plastic pan, as you hold your breath as you QUICKLY close up the boat without breathing. When returning, open the boat to 'air out' for a long time before reentering. Obviously para-formaldehyde crystals wont be available in states that prohibit the use of common 'chemicals' by consumers. Para-F is deadly to mold/mildew, and human lung tissue too.

;-)
 

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My method for 'killing' mold in cushions:
1. remove and wash the upholstery fabric

2. Foam cleaning
a. Roll up and put the foam into a large thick film plastic trash bag
b. Put a few tablespoons of ParaFormaldehyde (MildewGaz, etc.) into and wrapped into a paper towel. Insert the Para-F into the 'middle' of the foam 'wad'
c. Take the bag and foam OUTSIDE into the fresh air; close the trash bag around the vacuum hose of a 'shop vac' and pump all the air out of the foam inside the bag. Twist the bag to close off the shop vac hose and tie it securely closed. Remove the vacuum hose.
d. Let the evacuated bag sit for several days, re-evacuating when necessary - the bag still 'outside'.
e. after several days, remove the remnants of the paraformaldehyde, reclose the bag and pump down several times to remove the Para-F gas inside the foam.
f. Let the foam fully 'air-out' for a day or two before putting it in any living space.

2a. Foam only lasts a few years before breaking down and becomes 'softer' anyway; so, when you replace it, buy your foam with mildew retardant already included in the foam .... more expensive but certainly worth it.
 
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