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I know this is possible, but I can't figure out how to do this. 
I have MVP Baseball 2005 ripped from the disc. I have been trying to get into the game and change the rosters.
I found a way into to edit the game files, but when reassembling the game,  it's no longer treated like a game by PCSX2, it acts like I'm trying to play a bootleg disc.

Any ideas? 

I do own the game, and ripped it myself, so if this is a banned topic, I'm sorry. 

Thanks.

Use apache to edit the iso and make sure the new files have the same name and same size as the files you are updating.