Could you give us more information on how your image folder is structured? How are your folders and images named and nested? How are the images referred to in your attachments?

You may not want to use Flatten paths if you have images in subfolders that have the same name.

With Flatten paths unchecked, the names of the regions in the atlas are:

effect_A/power
effect_B/power

With Flatten paths checked, the region names discard the path, using only the image name without the extension:

power
power

This is not allowed

each region name must be unique. I assume you have Flatten paths checked, otherwise please post your settings. You can click Save on the texture packer settings dialog and save a .pack.json file with the settings.

For everyone who, like me, encoutered the same error and was unable to export single atlas for several skeletons. The issue was in the wrong path for source images for one of the skeletons. The skeleton was imported from another place therefore used a dublicated sourse folder with the images with the same names. Was resolved by assigning image path to the common to all skeletons 'images' folder