Now that you've deleted that folder youmay have to reassign your ringtones/ notification sounds.
When I did that, the files in those folders automatically showed up in the notifications and ringtones lists under settings as well.
Maybe this will work for you as well.
Brent D. Braaten
Proud member of the Droid Army.
I had this issue with my wifes eris. I had to actually make the folders first, then copy the ringtones into the folder. I had used a folder from my computer already filled and had copied that over to begin with and it dumped all the ringtones in the music list even though they were in a folder called ringtones.