ITunes loses original file!

Hi
I have used my iMac G5 for several years & have downloaded tracks from iTunes for a similar length of time. Tonight I docked my iPhone & got a message that 100 tracks could not be sync'd as the original file could not be found. I saw that this effected my whole music collection as a little was next to every track. I check the music file & saw that there were now music files on the HD!
I have backed up using time machine which seems to have sorted most but not all, especially those bought through iTunes over the last month, even though they are on my hard drive when I search manually?
Whilst it says that tracks have not been transferred to my iPhone, when I check they are there?
Any ideas of a) what caused this & b) how I can fix it once & for all. I am thinking I might need to uninstall iTunes & reload, however I have a long list of smart playlists I really don't want to have to set up from scratch again.
Help?

I just ran an update and iTunes would not play my earlier-purchased music. More recent music would play. Much of my music was backed up to an external hard drive, but some was not (by some we're talking 100 songs or so). So, I called Apple Care. The first guy I spoke to was clueless about the problem and tried to get me to copy over my music list with copies from the extHD. That didn't work and just gave me copies of files in locations where they shouldn't be (not good for an organization freak like me). The second "specialist" I talked to somehow lost a ton of my songs. I don't know what happened. They don't know what happened. And for all my TWO SOLID hours of trouble, the specialist didn't even call back last night as he promised. I'm trying to get a rebate from iTunes for the music that I purchased that was not backed up to the extHD (since all of this was caused by an update). This is a STRANGE problem. Next time, I will try the "fix" mentioned above - no one at Apple Care ever told me to try that. Until then, I am musicless and annoyed.

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