Tell me. I inserted a lot of side characters in here, but now I don't know what to do with them.... asked for advice in SHF, got sime tips, but not a lot....
You didn't get much advice in SHF because you started it off by asking whether or not you should kill them all. And I think the advice you did get was enough.
Was it, tho? To kill or not to kill. To eliminate or not to eliminate? Or to have them disappear? So many questions...
I always find it satisfying when everything, including the side characters’ arcs, get wrapped up in the end. See Dickens.
Just have them injured for a bit, break their legs. Or if you don't want to do that, you can have them do their own thing and be away from the main story.
Many stories do wrong when they have a lot of side characters, so what is the best option to do with them, let them be, kill them before introducing others. No, there is no best option, only the less worst option. The true best option is... Don't make side characters
If you don't introduce them to others to push the plot you call them "Minor Character", not side character. If they are killed or removed before pushing the storyline, then they are minor character. Also, there are no such thing as "Side character" they are either a misnomer for Major Character or Supporting Character. It's part of the essentials to create a story. Main character Major character Supporting character A story doesn't need to have Antagonist character, Minor character, etc.
The rule of the thumb is, that you need to ask yourself before you start writting that scene with the side character. if the character doesn't bring meaningful interaction in the scene/story: - to further the plot(main or the side); - help the characterization(himself, the MC or setup for the interaction with another character); - help worldbuilding or infodump; - or the character development then you can just never mention it again, depending on how important that character is. Most minor characters can just disappear in the background after they completed their 1 act to push the plot forward, or being there for the MC get a interaction with a major character. example :"The town villager chief that just there to tell the MC where the mine cave is to never be seen again". Also even if in the story logic, the MC would come back to finish the quest and talk again with him, you can deal with it offscreen if interacting with him doesn't add anything to the story then just cut it. In theory you can do it with any character, xianxias are master in never mention again some character, in special if they advance to a more powerful place and the previous characters can't keepup. Harem gang has the worse of it(most because they lose the little characterization they had when they are the target for the conquest. And become caring wife of the harem) But if you keep too many sidecharacter, they often become the popcorn crowd that their only use in the novel is to be awe of MC awesome action and make comments about the current fight scene and background of the character that the MC can't be bothered with. Better author at least use this moment to convey their personality, even if they can't be direct in the fight. Also some sidecharacter can still show up from time to time, the mentor usually talk once and is gone for dozen chapters before the next piece of wisdom is dropped doing his own thing, after all not everyone can follow the MC around and eat popcorn or be part of the harem. You can easy handle by saying they are working on their own thing, if is not already implied because they hold some position of power or skill. Just need to think deep when you thik on their impact in the story, plot and the "life" of the main cast. Example: "The father of the MC girlfriend" can be a nobody without even a name, can be a major antagonist or can also be just the quirky father in law that help characterize the MC and his girlfriend relationship and personality while providing some comic relif. How much he will stick around is only enough to fulfill whatever role he have that current make sense with the story, after all you don't bring your quirky father in law to the battlefield if he has no business being there. You still need someone to be the quirky guy you make someone else, and leave the previous behind or maybe kill them if that help further the story.