These weren't official updates. They were modified versions of the game file (usually an .swf file) that players would download and run locally. By bypassing the server verification (or lack thereof, since it was often a client-side game), hackers turned the experience from a strategic RPG into a power trip.
"Hacked" versions of this Flash-based game generally include a or modified UI that allows players to manipulate game state variables in real-time. Common modifications documented in these versions include: Resource Manipulation : ben 10 omniverse galactic champions game hacked