The only way to remove a rust pit is to take the surrounding surface down to the same level, or else to try and fair it out so the low spot is less visible. Depending on how deep it is, that could mean losing engraving or altering barrel diameters etc.
You may end up making a decision to cut the small marks out and accept that the deep stuff is there to stay. Treat it as part of the roadmap of the guns life and do the best that can be done for the rest of it.
Do be careful with keeping sharp edges sharp, flat surfaces flat etc. It is easy to take metal away, not so much to put it back again.
Some helpful stuff
https://www.firearmbluing.com.au/art...t-blue-recipe/
https://www.youtube.com/watch?v=O4QOcRTZv2Q&t=903s
Cleanliness is essential, and don't go putting too much solution on the steel at a time. Using the steamer speed things up, so just take as much time as it takes. A box of cheap vinyl gloves are handy.
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