450GB of my data erased by Itunes update. This is unacceptable.

Digital goods are particularly fragile. I have research data in the form of podcasts on my computer from the last seven years of my work. MANY of these files are irreplacable! A simple update of my application software should not be ABLE to erase that data from my computer, yet that is exactly what happened. So before any of you start talking to me about backups and system settings, let me say that I do have a backup. That is not the point at all and because I will be able to recover my data eventually does not minimize in any way the seriousness of this situation. At present I cannot work and my attempt to talk to someone at Apple will cost me $20 bucks, only for them to "apologize" and tell me to restore my data from backup.
If I replaced my refrigerator with a new unit, there is no possibility that all of the food in my house (worth hundreds if not thousands of dollars) would disappear. Am I to tell my hungry children "I apologize"? Yet that is exactly what occurred.
So what I need to know is what settings on my MacBook Pro need to be changed in order to prevent Itunes from deleting data without those data files being in the Trash can? So once I retrieve my backups which are kept off site and go through the 7+ hours it will take to restore how do I know that Itunes will not delete them again? This has been reported by many users here on the support forums.
So can anyone help with suggested settings?
Can anyone help me recover the lost time and productivity?
I own many apple products, and have for years been an advocate for them. This is the worst customer service experience I have ever had.

First of all, let me say I can totally relate to your situation. I lost 485Gb of music and audiobooks (albeit not to an update, but bad hardware) and I had the same experience when seeking answers, only it was Western Digital who told me, "We're sorry your 60 day old hard drive seized up, but we can't (translation: WON'T) do anything about it."
Unfortunately, I was in the process of moving my 485 Gb backup to the WD hard drive when it seized, and I lost all of it, because the drive I was moving from was going bad too and wouldn't restart after reboooting. Moot point here, because it's apples to oranges, but yes, backups are lifesavers.
I have a rule about updates: I go "barebones" for anything OS or major software related. In other words, except for my mouse, keyboard and monitor, NOTHING is connected to my Mac or my PC when I run updates. In a worst case scenario, I only have to reinstall my OS and apps. All my documents, videos and music are intact and isolated.
I know that doesn't help with this situation, but going forward, it maybe something to consider.

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