As Aaron said above. Oftentimes, the Finder simply lies about what's there, which is an old problem and nuisance, but only a miracle will give us a better Finder. That's not helping you...
If you really lost files, this app works pretty well:
http://www.prosofteng.com/products/data_rescue.php
You can try it on a few files and only if it works you have to shell out the dough. Saved me a few files...
In case it is Finder having a brain fart, which I would not be surprised about, you may want to consider this. In Terminal, type:
defaults write com.apple.finder QuitMenuItem 1
Then log out and back in, and you'll have a Quit menu item for Finder. When you think it's lying to you, such as with network file systems but also in general, simply quit and re-launch it and you'll get a fresh look at the filesystem
Yes, it would be nice if there was a simple "Refresh" or such menu item, but clearly this is more user friendly