As of 9 November 2024, the developer pushed out an update that removes the executable files, putting them behind the "LWJGL3" beta toggle. If you want the EXE files back, simply enable that toggle. The developer claims that this fixes the whole issue, but some people are still reporting false positives. If you're one of these people, or you wish to use the executable instead of a JAR file, simply follow the preceding steps.

1. Open up Windows Security and click on "Virus & threat protection".
   
2. Scroll down to the "Exclusions" section and click "Add or remove exclusions".
   
3. Click "Add an exclusion" and then "Folder".
   
4. Find the "Age of History 3" folder (you can easily find this by going to the game in your library, clicking the gear, going to "Manage" and clicking "Browse local files"), select it, and click "Select Folder".

This should prevent Windows Defender from scanning the folder from this point onwards, removing the likelihood of any and all game files being deleted over false positives.