I know what they did, and I found out completely by accident.
I was playing as a Biological with a HUGE damage chain, and was fighting Captain Hunt. He used Desperate Shield and I blew it open in one move. Then Roald and the Captain had a little dialogue and the battle ended. So I think they modified some of the battles.
There was no updating for Sonny 2, if I'm not mistaken there was an updating in the AG site, they just changed the folder's name that keep the save files, they do not got erase, just make a search for this folder: "armorgames.com" All your save files from all games will be there. They changed the folder "armorgames.com" for "cache.armorgames.com".