what are you using to delete the ringtones? make sure the app has the right permissions (root) to be editing things in the system partition. you can also delete the ringtones from twrp
Same app I've used for years. FX (File Explorer). This was happening on the internal sd card first. I only went to the /system partition to see if that would change things and it didn't. Never had issues until today. The ringtones were gone.. but it's like the media scanning wasn't refreshing even after reboots. First time I've experienced this.
IDK, long story short it seems to be working now. After clearing the app data of media storage and rebooting the updated list appeared in sound settings. I also updated to your 8/25/17 build.