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Just take them out spray them down with Lysol and let them air out for a day or two. You can also spray them down with Febreeze after the Lysol treatment to add a nice fresh smell. It works for me. BTW, my bag liners have no cardboard inserts; they're just textile-type fabric, with the HD logo, and molded to fit the cases.
Of course, nothing should ever be packed away wet and left that way. It's like stowing your tent when it's wet, you must unfold it and let it dry as soon as you get home.
It seems like you're talking about the removeable liners which are like luggage . You need to soak them in something that will eliminate the mold. A mild solution of water and vinegar or ammonia should do. Rinse thoroughly and air dry comlpetely. Your rain gear would probably get clean in the wash and I'd add the same diluted solution you used on the bag. Good luck. Let us know what happens.
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