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I'm not sure I follow you. If the jars are not sealed then microorganisms will get in after the jar cools off, period. I don't see why they wouldn't Wouldn't that layer of salt also keep out the good microorganisms that are necessary for fermentation?

Since you don't seal the jars, what's the point in sterilization? I would think that the ambient microorganisms that get into the jar after you sterilize would be exactly the same as the ones that are on the chiles before sterilization.