UPDATE: Issue described below still exists, however I've created a tool that can work around it; Keep My Mod.
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Now that 2K has started updating/fixing things besides just adding new stuff using the Online Data silent downloads, this means that any mods we install are overridden.
Example:
Pistons court floor file f021.iff. No matter what mod you use and how you edit the f021.iff file in the game's folder, if there's an f021.iff file in the %appdata%\2K Sports\NBA 2K12\Online Data\download folder, the file in the game's installation folder is overridden, ignored, and the game instead uses 2K's update.
Replacing the file in online data doesn't work either, as the game likes to delete the whole "download" folder and re-download everything if it finds something going wrong in there, of if it can't get a connection to 2K's servers.
Btw, the Pistons floor is not a hypothetical example, it was actually updated in one of the last Online Data updates, and now we can't use any custom Pistons floor, as the game will always use 2K's own update instead of the mod.
The only solution is to prevent the game from connecting to 2K's servers, but that means no online, no living rosters, no NBA Today, no other updates.
We need to find a way to keep this from happening, or to make a tool that will start the game, allow it to update, find out when it's done updating, and then delete from the Online Data folder whatever files the user wants to keep using modded.
There is a way to find out when the game's done silently updating (as the game's front-end doesn't inform you about this). It's the moment the folder %appdata%\2K Sports\NBA 2K12\Cache\patches gets deleted. That's when all new patches/updates/additions are copied to the %appdata%\2K Sports\NBA 2K12\Online Data\download folder.
So we need to make a tool that will keep a list of the mods the user has installed, allow them to start the game, watch for when the Cache\patches folder gets deleted, and delete the user's modded files that got updated by 2K from the Online Data\download folder.
I will be trying to do that, I have enough programming experience for something like that, but if someone with more experience wants to do it, all the better.