I'm not familiar with your project, so I can't tell what is "corrupted". Can you explain what you mean?
Edit: If you mean the atlas data looks different, that is the new format. It is half the size, allows the format to evolve without breaking existing atlases using the new format, and allows arbitrary name/value pairs per region (useful for frame-by-frame animation, among other things). If you want the old atlas format, check Legacy output in the texture packer settings.
