It looks like the images are fully transparent but still contain color data. My tool can make this easier to deal with, but the settings I mentioned above are wrong for this case. This will only work if they are invisible when dumped.
To get them to show up:
- Find the problematic textures, get them into a "Texture Path" for my script
- Select the operation "PNG Alpha Pixel Manipulation"
- Use "Remove Full Transparency from Color Pixels"
- The resulting textures should be visible
- Perform an upscale on these textures
To get them back to their original state:
- Grab the upscales, get them into a "Texture Path" for my script
- Select the operation "PNG Alpha Pixel Manipulation"
- Use "Add Full Transparency to all Pixels"
- The resulting textures should be invisible
To get them to show up:
- Find the problematic textures, get them into a "Texture Path" for my script
- Select the operation "PNG Alpha Pixel Manipulation"
- Use "Remove Full Transparency from Color Pixels"
- The resulting textures should be visible
- Perform an upscale on these textures
To get them back to their original state:
- Grab the upscales, get them into a "Texture Path" for my script
- Select the operation "PNG Alpha Pixel Manipulation"
- Use "Add Full Transparency to all Pixels"
- The resulting textures should be invisible