How can I jailbreak my switch without affecting my brother's switch in the process?

In these situations, there is no way of knowing without doing it, and even then, Nintendo might change it later on (I would imagine that even in the best case scenario your brother's account will have a note on it that it is associated with a hacked console, and Nintendo might decide in the future to ban any account that has even a little smell of a hacked console).

I hope you know that homebrewing/jailbreaking your console will void any warranty, and comes with big risks of bricking your console.

So if you jailbreak/homebrew your Switch, be ready to lose both accounts and everything bought on them.

Just to give you an idea of the lengths Nintendo goes to screw over those who play 'outside the bounds', every physical game of switch comes with a unique code, and they can straight ban every single copy of that cart if they see one that weirdly starts popping all over the place, and I guess put a notice to every account that loaded it. On that console, Nintendo shows that they are not messing around.

And really, its not like you dont have other options if you want to emulate oldies. Emulators up to N64 run on about anything (phones and computers) and they don't come with that heavy caviat.

TLDR: Don't do it, you will probably destroy a 300$ piece of hardware and lose anything bought with accounts that have touched the console. If you want to play old games, get an emulator elsewhere.