Personally, I don't have an iPhone. But are you sure that the files are gone COMPLETELY? If they are not then you have to get rid of them first.
Can you play the ringtone on iTunes when the iPhone is not connected? If so then the file is not gone and you have to find it.
This is just a random guess but maybe every time you connect your iPhone and sync it with iTunes the ringtones from your iPhone go to the ringtones in your iTunes library.
If any of this works let me know.
If not... then you wasted a lot of time.