I have some files in a local workspace that were checked out and then deleted but were not deleted through TFS. TFS still has them marked as "edit" in the pending changes view. When I try to check-in the deleted files, I get an error saying the files cannot be found. Is there a way to tell TFS that these files have been deleted and that they should be deleted in source control as well?
You could, through team explorer, right click on the deleted files and do a undo pending changes.  Then through team explorer delete them and check them in.
If that doesn't work - right click on the deleted file through team explorer; do a get specific version and check both checkboxes to overwrite files:

This will fetch the deleted [from workspace] file from TFS.  Perform an undo pending changes on the file.  Then delete the file through team explorer and check it in.
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