You could try chasing them with a nut as it would "reform" the thread instead of cutting away the damaged metal.
A regular AN nut will likely work better than a stainless nut as there is less chance of galling.
There are also "thread repair" dies available that again would reform the metal instead of cutting it away.
In any case, use some lubricant.
Last resort, better to fix them with a carefull application of a jewlers file. Note there are thread repair files that work well though, if the damage is localized, I've used a jewlers file under a magnifying glass.
I can pretty much guarantee that if you run a standard die on them it will take extra metal out, basically converting them into cut threads and the associated drawbacks
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