When you delete a file in Eclipse, it is deleted from the CVS repository when you commit the change (by committing the folder). But CVS doesn’t destroy the file, it puts it in the ‘attic’. If you ever need to get that file back, you can.
From the context menu for a directory or package, select “Team > Restore from Repository…”. You’ll see:
On the “Restore from Repository” dialog, select the resource and version (you get a preview) and click “Finish” to load the file into your workspace. Once you have the file in your workspace, you still need to commit it to put it back into the respository.