Sure they could... the problem is just that apparently no structural changes were made during the cleanup, but the wave was there before they turned the water off and gone after they turned it back on. And they don't have to wait for a year, they can adjust the flow - the wave is situated in a "brook" very near the point where it exits a tunnel through which it flows under much of the city, so it's heavily regulated (see this map for all Munich "brooks" on the West side of the Isar:
https://upload.wikimedia.org/wikipedia/commons/f/f3/Karte_M%... - blue are the current ones, dark blue is in tunnel, the purple ones are historical, the Eisbach is #55 in the top right corner).