No,the r4(Or "flashcard" as is better known) doesn't damage or brick ur 3ds. If u buy a Flashcard for DS roms,it'll allow u run DS games on ur console. If u buy a Flashcard for 3DS games,it'll allow u run 3DS games on ur console. I Recommend use just the DS Flashcard,cuz it's unnecessary buy a 3ds flashcard,we have the CFW nowadays for 3DS.

My best suggestion is to CFW the Nintendo 3ds with this link ,and exists the TwilightMenu++ for cfw users,this app'll allow u run natively DS games on ur 3ds without a Flashcard

 

yep,but if I read right,he doesn't have both(3ds and flashcard),so,my suggestion is to use twilightmenu++ instead of flashcard(mainly cuz twilight is free). If this isn't the situation,just ignore the Twilight part and use the flashcard