What's wrong with taking it out in the HOME Menu? Had my consoles for years, I hotswap SD cards at least twice daily, no problems. As long as data isn't being downloaded via SpotPass, you'll be safe.
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"two months ago"
Well sir that is your problem. It would be completely useless back then, emuNAND literally runs live off the SD Card, and that's how everyone used CFW. Now that a9lh is a thing, we can remove the SD card while in custom firmware.