Any files that the version control system thinks should be there, but that can't be found in your working copy are shown as “Missing” under “My work”. All you need to do is:
1. Find your file in the “Missing” list and select it
2. Click Remove in the toolbar on the left of the window
This tells Mercurial that you haven't merely lost the file, but that you intended to remove it. The next time you commit, it will be removed from tracking in version control.