Deleting the default sounds folder is not a problem, since when running on default, it only contains a "token file" anyway. The default sounds are "stored" in the sounds.res file in your game install. If you do not have a sounds folder upon starting the game, AH will automatically create one with the token file and use the sounds.res file to play default sounds.
Make sure youre custom sound pack folder is called "sounds".
BTW, which custom sounds are you trying to use?