I saw that some of my POIs are 2 MB. At first I thought it was the big POIs but not. It was some big and small. It is the same POIs from my previous scenario Conquer 2 and that scenario is only 26 MB and has more POIs. The Prefabs folder in Conquer 2 is only around 8 MB but in scenario Conquer 3 is 94 MB. There are no pictures in the Prefabs folder. I need to add more POIs but instead I had to delete POIs.
I found a solution: Running the latest experimental branch, logging into the game and resaving all the blueprints reduces the file size back to where it should be. My scenario prefabs folder went from 33mb to 2mb after doing this. I was about ready to scream internally.