so cheats messed up the game so i tried deleting the rom and downloading it again but that didnt work. i tried that with the emulator too but didnt work. there is no folders tab too on the settings
Delete the specific save files pertaining to the game in question. Project64 stores these in the Save folder by default. You can check in which directory the saves and other data saved to by looking at the Directories tab under Settings.
but nothing's in the save folder, i use native saves. i just deleted the native save file, but will that restore my rom? or is it still affected and messed up by the cheats?
*and btw this is dk64, i cant unlock mystery mode, i have 10 banana fairys already.*
All native saves as well as save states are saved in the Save folder, and the only exception is when a game uses the MemPak for saving game data.
Note that cheats do not alter the ROM itself (unless intentionally hacked to include cheats on the fly), cheats alter the memory addresses the game uses when running. So yes, after deleting native saves and save states (which save memory addresses), your rom is "restored".