Are the files really missing? Look in the Media folder in the iTunes folder. It is possible only the reference to them is bad. iTunes does not do this automatically and you omit to tell us if you have recently upgraded or something.
If they are really missing 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. 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