Hi David Cronin,
Regarding the deletion of tasks, TeamPulse does not hard anything in Tfs which is why the delete option is disabled when a story is syncing. The preferred approach is to mark the status of the item as Deleted.
Regarding the burn down not hitting 0, this might happen if for example you had a story for Iteration 4 that was set to done after the end of the iteration. Because the burn down chart is constrained to the start and end dates of the iteration, the post iteration status change of the story won't be picked up. Such a status change would show if you viewed the burn down for a parent iteration. Might this be describing your scenario and explaining what you are seeing?
the Telerik team