You can remove the SD card from the camera in emunand, reinsert the sd card, then go to the home menu. The only issue is that your theme will reset until you reboot, or change it again. You can probably do the same with a ciaWait, what? You want to unmount the SD card *on EmuNAND*? You know your whole EmuNAND runs from there?
Let me rephrase that for you... would you ask how to unmount / switch the hard drive from Windows?
And, this only works from my tools, because my tools run from an area that is mostly separate from the 3DS firmware.