I'm not getting it. You're saying that I should restore and set it up as new but then loading the backup anyways?
Alright. Let me elaborate this for you.
In my experience, when I delete everything inside "iTunes_Control" folder, all music, custom ringtone is gone.
Then, when plugging it into iTunes, iTunes will recognize this device as a "new" device, and prompt you to choose "set up as a new iPhone" or "restore from backup".
Obviously, my device is not a new device at all, and I don't restore it to factory settings. However, to pass this prompt, I need to choose "set up as a new iPhone". I dare not choose "restore from backup" because I am afraid it will really restore from recent backup straightaway.
The fact is: nothing happen. iTunes does not change anything on my device.
Long story short: I don't do a restore. I just delete everything inside "iTunes_Control" folder using iExplorer so that iTunes library on device is effectively gone. Then, I sync my music back, as well as ringtones.
Hope I am clear.