Move it to the pillaged tile and it should give you the option to repair. Turning on the tile yield icons in the map options will show how much food, production, culture, science, and faith a particular tile is worth while being worked. The description for flood barrier says: “If constructed after some of the city’s tiles have been flooded (but not submerged), those tiles can be repaired in full and used again, along with all that’s on them.” What do yield icons mean Civ 6?
You have to go to your city’s production tab and click on the relevant district or building to repair it. Just to add to what everyone has said around pillaged improvements, pillaged districts and buildings are repaired differently. How do you repair pillaged land in Civ 6? Wonders can’t currently be pillaged or destroyed, except perhaps by nuclear weapons or by razing a city.