The nature of the sync is to make sure your library and your device have the same contents (more or less minus manual changes). Do you not want your device to match your library?
If you have content on your Zune but it is not on your PC, perform a reverse sync. As soon as you plug in the Zune, look for the Stop Syncing button which will be in the lower right corner of the Zune software. That should stop it from erasing content.
Open the Sync window by clicking the button that looks like two arrows chasing each other. Drag the content that is on your Zune but not on your PC to the Sync window. In the bottom right of the Zune software the sync button should now be changed to Copy from device.
Once all of the content from your Zune that you want on your PC is in the sync window, use the Copy from device button to transfer it. Get the rest of your library in order and when the library looks like what you want on the Zune, perform another sync so that the Zune and your library matches.
If you have content in your library that should not be there, you may want to check the Monitor Folders settings in Options and make sure you are not monitoring unwanted folders. If there is content in a monitored folder you do not want in your library, manually delete it from the library but do not delete it from the hard drive. This way, you can always add it later and you keep a copy.
You may want to think of your Zune as a portable extension of the Zune software. It is not really autonomous in that it can't manage, edit, etc. content on its own. Essentially, it is just supposed to be your hand held media library. If the library on your PC is not what you want "in your hand", you will want to work on getting the library exactly as you want it and then just let that flow to the Zune.
Hope this helped.
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