The general principle by which this operates is described here (it is similar in Scotland - allegedly).
http://www.onlineplan...eservation_orders.php
You will note that it is the local authority itself that decides whether a tree or trees are worth preserving - often as a condition of a planning consent that might threaten them.
You don't unfortunately say very much of an objective nature about your local council's flood defence programme ('laughable' is rather subjective) - but I'd be inclinded to research the project that they have announced - it must be been the subject of an Environmental Impact Assessment to have got this way - that's the way to try and get it overturned - not via a few random TPOs.