To help keep track of entities you've already found, you can mark them as "Complete" using various interfaces like the Sidebar and Context Menu.
You can complete entities in bulk using Data Tables. Mark multiple rows then select "Complete Entities" from the toolbar. Similarly to reset multiple completed entities RightClick or LongPress "Complete Entities" instead.
If you want to re-play a game and clear all of your completed entities, you can do so from Game Preferences.