Yes.
If it is an S-ability that you would like to use somewhere else, or which is hard to find, you may swap it first to another weapon (like a Val if it's S1, S2 or S3). The cost is around 1 million though, so if it goes in the market for like 900k, it's more "beneficial" to actually destroy it and buy a new fodder with the lost S-ability.
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