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?
3 Answers
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.
I think you should be able to do this via source control explorer: View -> Other Windows -> Source Control Exlorer. Find the code file that you want to mark as deleted and right-click and select delete.
For future reference, TFS Power Tools is very useful for this kind of thing.