I think the uninstall asks if you want to keep your savegames.
Yes, it might be because you use a crack. Some patches are also verifying the file integrity.
I always make a backup of the original exe. When I want to install a new patch, I don't have to reinstall the game. After I patch the game, I make a backup for the new exe(the patched one), replacing the original version. I repeat this operation every time when I apply a patch.
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