Help: iTunes wants to delete all my music and videos off of my iPhone!

I usually keep the option to manually manage music and videos on my iPhone. I only use 1 pc to transfer music and movies to and from my iPhone. Recently for some reason when I launched iTunes, an error message kept poping up repeatedly saying "The iTunes Library file cannot be saved." I fixed the error message by adjusting the user access privileges to my music folder.
Now my music library is completely empty in iTunes, but that shouldn't be a problem because I manually manage my music and videos. However, when I checked the iPhone page in iTunes, the checkbox for manually manage music and videos is unchecked.
So I went to go check the check box so that I can continue to add some more music and videos to my iPhone, however a message box pops up saying:
"The iPhone "my iPhone" is synced with another iTunes library. Do you want to erase this iPhone and sync with this iTunes library?"
I have about 12 gigs worth of music and videos which I have carefully hand picked over a period of about 3 months and now iTunes wants to delete all of it because it thinks I want to "sync with another library". I only hope someone can understand how frustrating this is for me. All I want to do is continue to be able to add music and videos to my iPhone without having to erase months worth of work putting the current music I have on there. Can anyone help me?

Thanks for your reply. I don't keep all of my music in the iTunes' designated music folder. I don't like the way iTunes reorganizes my songs and I keep all my music in my own self organized music folders as I don't use iTunes as my primary media application. Not to mention allot of my files come from all different corners of my computer's hard drive. It would literally take months to go through over 20 gigs of media files to pick out the songs I have in my iPhone library to rebuild an iTunes library. Like i said, I don't even use iTunes other than to transfer files to my iPhone. I thought the purpose of manually managing the files was so you don't have to sync it with the iTunes library but now it won't give my that option without requiring me to delete everything on my phone I worked so hard on.
What I don't understand is logically or technically why iTunes HAS to delete all the content off of my iphone. Who's decision in the Apple's software engineering department was to require the one's iPhone to be erased if someone loses their iTunes library? Its frustrating because it makes no sense and I feel as if the software is punishing me for reasons I don't understand by threatening to delete all my content off my phone. Is there absolutely no way to transfer my music to my iPhone without deleting everything currently on and completely rebuilding my music library from scratch?

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