Removing the folder will just make players don't receive the "mail rewards", this is the function for the folder, to hold the mails.
if that is what you want then the answer to your question is YES.
Removing the folder will not remove the request for master inside the game, any player will still be able to request/have Master, neither will remove other rewards that are not typeof mail (like for example MP reward, lvl reward etc). to remove those you need to complete disable Master/Disciple at server side (best way) or client side(not recommended by me).
To remove on server or client, just debug the .exe, find the offset where the function start and jumped to the end of the function.