They would lose any magical powers they may have had in the book, but anything they are, rather than can do, will stay. For example people from the His Dark Materials world would keep their daemons. You can take them out at any time in the story’s plot, but for all other people consuming the media, it will be shown that the character suddenly disappears, with the rest of the plot being affected accordingly. People will notice this happening. The character is not under any sort of control by you once you have taken them out of the story, although they will appear next to you to start with.
I don’t know if it counts, but if I had enough radiation protection, I’d say Urayne from Pokemon Uranium just after you defeat it for the last time and are given it alongside the core that allows it to essentially live forever. Though, I assume by that point you wouldn’t need radiation protection considering you never see the player character pull out the advanced radiation suit when you gain access to use him in battle.
Don’t know if doing something like the one time Curie did that quantum leap would count as a magical power, but imagine how cool it’d be to be able to teleport anywhere (depending on if quantum leap has no limits on distance) for free.
Also, I’m sure this would count as a magical power, but unlimited nuclear energy for free would be amazing.