its useful for devs who want to test things but for the average user it really isn't something worth setting up. unless you're really paranoid about bricking your sysnand then just stay away from making an emunand honestly.
if the file you deleted had three question marks then you deleted the system transfer app. i dont think you can recover from this since you deleted a system title.
edit: im dumb ignore this
exactly who does this effect? it cant be people who inject legit mons since the number is only 6k. is it injecting things like clothes/items which triggers a ban?