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