I Tunes has lost a large proportion of my music library.  The music in question is however still on my IPod.  Is there any way to sync backwards so the IPod updates ITunes?  Or is there any other way I can try to recover the lost music files?

I Tunes has lost quite a large proportion of my music library.  I think this may have happened when I tried to download a previous version of ITunes that failed to load.  Whatever, the music is still on my IPod.  Is there anyway files on an Ipod can be transferred back into ITunes?  Or is there any other way I can try to recover my music files?  Also, I no longer have any confidence in ITunes ability to store data efficiently and wonder if there is any way I can back up my IPod outside ITunes?

Your i-device was not designed for unique storage of your media. It is not a backup device and media transfer was planned with you maintaining a master copy of your media on a computer which is itself independently backed up against loss.  To use a device with a new computer you transfer the content from the old computer (or its backup) directly to the new computer, not the device to the new computer. Media syncing is one way, computer to device, updating the device content to the content on the computer, not updating or restoring content on a computer. The exception is iTunes Store purchases which can be transferred to a computer.
iTunes Store: Transferring purchases from your iOS device or iPod to a computer - http://support.apple.com/kb/HT1848 - only purchases from iTunes Store
For transferring other items from an i-device to a computer you will have to use third party commercial software.  See this document by turingtest2: Recovering your iTunes library from your iPod or iOS device - https://discussions.apple.com/docs/DOC-3991

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