don't worry. there will be no issues if you follow the guide correctly, so be carefull.
the part of downgrading to 2.1 involves downgrading emunand, unbricking emunand(100% safe since this is emunand) checking that every emunand title is validly downgraded, injecting to sysnand, then checking that every sysnand title is valid. this ensures you on that everything is ok. although, if your 3ds blackscreens, take the SD card out. i've installed a9lh on 3 different consoles, and every single one would not boot with the SD card in.