Just leave it there, It's not too big of a file anyways. But if you really want to delete it, Just make a backup of the 2 files(the one you didn't replaced) somewhere on your computer, delete it from your SD, plug it to your n3ds and if it boots menuhax to properly, then your good to go. Just remember to place it back again if something is not working. That's how I did anyways, but in my case, there are just 2 menuhax payloads.