If there are custom tones on the device that don't show in the iTunes interface, or show up as greyed out tracks that you cannot remove, you could use iFunBox to poke around in the file system of the device. (Decline any special offers while installing.) In iFunBox try Toolbox > User File System > iPod_Control > Ringtones. Any custom tones on your device should probably show up there with random 4 letter file names and a .m4r extension. Deleting these should clear all custom tones from the list on the device, and you can then try adding back what you want using iTunes.
When adding back start with a small selection rather than all 600.
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