There are 2 ways you can delete a file from the library.
1) Delete from the library but keep the file in the hard disk.
2) Delete from the library and from the hard disk.
If you've checked the box "Also delete file(s) from hard disk, it means that the file has been deleted completely. If not, you still have the file in your hard disk. You can search for the specific song in the location where you originally stored it.
Would you know how you might have deleted it?