You can try to recover lost files by following this article.
In short – I’d probably try with this program – Recuva – from piriform that also makes ccleaner. That is – only if the file is not that important. If the file is very important follow the steps where you load a live ubuntu.
Revuva will scan your harddrive – or – USB pen, to see if there are some files that it can find on the drive, that are not showing up when you look at the filesystem.