1

In older galactic wars, when lightsabers are prevalent on both fronts, it was the norm for militaries, private security forces, bounty hunters and other adventurers alike to arm themselves with weapons and armour protected by a cortosis weave. So cortosis is not exactly rare, since it can be used in mass manufacturing by the war industry and is accessible to common use by private individuals too.

Since the Separatists are preparing for war with the Republic and its Jedi guardians, and the Sith plan to use the Clone Wars to help wither the Jedi down by attrition, why aren't lightsaber resistant troops more prevalent? I would expect super battle droids or at least more elite droids like destroyers, commandos, magnaguards etc to be so.

2

It was too expensive.

I think Wookieepedia explains it, the fact that it was rare and very expensive to make.

Earlier it seems that it was fairly abundant. Cortosis weave was in use as early as 4000 BBY as both an armor underlay and for the tempering of traditional melee weapons against lightsabers. At this time cortosis ore seemed to be much more common

But, became rarer,

later, however it would become a rarer, more valuable material that would give the user an unexpected edge against a force-sensitive opponent.

Also around the same time of the Clone Wars, cortosis shot were used, but that also states that they were very expensive.

used by Cad Bane in 21 BBY.

However, Bane stated that the bullets were expensive and hard on the slugthrower's barrel

So I think the general consensus is that it was just too expensive and rare to be mass produced by the time Clone Wars came around.

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