Open FBI. Go to "sd", press A on arm9loaderhax.bin. Select "copy". Back out and go to the main menu on FBI. Now select "CTR NAND". Click on "<current directory>". Select "paste".
Take out your sd card and boot your 3DS. It should pop up another menu for Luma3DS 6.6. Select "show system version/string".
Now when you boot without your sd card, you get a "clean version" without any hacked items...