Hundreds of missing files in iTunes (!)

My iTunes library is now showing lots of missing files with the ! next to them. I haven't moved my files or library. I have checked and the files are actually gone from the folders.
Question is: I have iTune music match enabled. All this files have an iCloud status of Matched or Uploaded. Why can I then play the files if they are in the cloud? I thought that that was the main idea of the music match, to safe keep copies of the files in case something happen (like this) to my library. All the missing music files are also in my iPhone but I don't believe I can synch and transfer those files back to the Mac. I will have to painfully look thru backups and find the files one by one and restore them to the respective folders.
Is there a way to restore the files from the iCloud/Music match library back to the Mac?
Thanks
Leo

I don't have a complete answer.
Changing preferences won't reconnect broken links.
Too many things happening at once so I can't tell if it was iTunes that did it or Tidyup.  I never let that kind of utility anywhere near my computer.
Letting a startup drive even get near the point where it is reporitng as full is going too far.  Never let it go much under 20 GB free at all times.
Your profile says you are running OSX 10.4.11 If that's true then there's no way you are running the latest iTunes upgrade.
You may have to restore the files from the second hard drive you bought at the same time you purchased hte first one since you always have multiple copies on different drives.

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