If you're lucky you will be able to recover a few files, but as long as one single file from any game is corrupted or missing, most probably the game will not boot (Maybe you will be able to extract the save with JKSaveManager even without the game not booting, at least you can try recovering the savefiles so you can inject them back after reinstalling the game). At least you are using arm9 and Updated Sysnand, this could have damaged an existing Emunand.
There's a reason why there's safety remove and why Windows won't let you extract delicate devices while still in use. Make sure to properly take care of your SD from now on.