Even after the incident earlier that morning, the harvest process did not stop and continued after the event was over. Elaina was thankful that the Merfolk that attacked earlier did not do anything to the baskets containing all they harvested. They might have attacked the farm but they are not after the vegetables at all.
When the sun starts to set, the work on the farm has finally concluded. All the plants that will not survive the change of seasons are already harvested from their fruits and are cleared off. They will start wilting and die once the next season comes and so before the next season arrives, clearing them off is much better than letting them continue to remain.