Apple iTunes software doesn't transfer songs to iPod from more than a single computer. When you upload some files from your computer to your iPod Shuffle (using iTunes), and then you want upload music from another computer, iTunes show an alert message detecting that you try to use your iPod in a different computer. If you accept this message, iTunes delete all the music tracks stored in your Shuffle to "update" the iPod content.

In the "/iPod_Control/iTunes" folder (a hidden folder) there are many different files used by the iPod device. But, the most helpful for iPod Shuffle is the "iTunesSD" file. This file store a tracklist with all the files located in your "/iPod_Control/Music" folder. iShuffle generates the "iTunesSD" file using the content of another folder (the "Music" folder) in only ONE STEP!
"The Apple logo", "iTunes" and "Shuffle" are trademarks from "Apple"

iShuffle works differently !
To use this simple software, you need first create the "Music" folder in your iPod root folder (\Music).
Save all your audio files into it, and Run iShuffle

Now you can play all these music tracks in your iPod Shuffle!! (and of course.. you can repeat these steps on another computer without loose any music file!)

NOTE: if you delete some files from your "Music" folder, or rename a file, you need to run the software again, to update the iPod Shuffle tracklist.