If only you use that computer, you could have accidentally deleted it when deleting a directory (assuming it was empty or unnecessary).

Another option I think of is that you were working on a file that was not on a hard drive but on some removable device (like pendrive) and it is still there.
(but drive was removed)
That is more likely, because I heard of such things when I worked in helpdesk.

There is also a slight possibility of a virus/trojan but even if I don't think it is a case, you may consider a good scanning.