I’m a physical chemist by profession and have worked with waxes and advanced lubricants and emulsions for most of my career. And raced most of my life. A great conversation here, and only a few small points I might add:
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The sediment at the bottom of the wax does contain a lot of the molybdenum disulfide and other floating or emulsified ingredients that settle out quickly. If you dump that, you dump part of the high-zoot lubricity-enhancing additives in the wax and thereby compromise the quality of the lubricant. Better to be sure the chain is clean when it goes in.
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Not withstanding comment #1 above, no matter how clean one tries to get a chain, it still contributes contaminants – not just grit but also organics that compromise the wax and how well it adheres to the steel of the chain. In fact it’s likely the stuff you don’t see that has the most detrimental effect on lubrication and component longevity. And strip chips use a grease sequestration component used in restaurants to congeal fat for disposal – they work well but are far from 100%. Now waxing a chain doesn’t have to meet infinitesimally precise standards but cumulatively strip chips do compromise the wax faster. Silca converted a lot of people to wax with strip chips because they made a slightly intimidating process much easier, but at the cost of quality of waxing and shorter wax lifetime. I have tested strip chips and find the properties of the wax change significantly after even a couple chains – not to where the chain isn’t lubricated adequately but the result declines in quality quite rapidly. And after a half dozen, Silca recommends replacing the wax – which tells you something about them. The lubricity becomes lower (i.e., components wear faster) first of all and then, more gradually, the longevity of the wax job decreases. This is where advertising tends to focus on certain characteristics while ignoring others.
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The waxes that carry the key lubricity ingredients are thermally extremely stable so repeated heating (and over-heating) have little adverse effect. The same is true of at least most of the identifiable lubricity ingredients – one can’t see all the potential contributors in a product data sheet, especially those that help emulsify or suspend key lubricity ingredients. So I wouldn’t worry about how many times the wax is heated, rather how many times any potential contamination is added. However, overheating the wax can remove some of the emulsifiers and other components that go into the wax and change how it works, so I’d be careful with temps – an Instant Pot can go up to well over 200 degrees Fahrenheit which is higher than you really want your wax to be.