When you replace exported files in Unity, it is important to ensure that Unity properly recognizes and imports the new files. If you manually copy the files into the existing directory, Unity might not automatically refresh the asset database, which can lead to issues like the one you described, where only the first texture is loaded and the second one appears pink. This is because Unity might still be referencing the old asset data.

To resolve this, you can try the following steps:

1. After copying the new files, switch back to Unity and force a refresh by right-clicking in the Project window and selecting "Reimport" on the folder containing your assets.
2. Alternatively, you can delete the old files from the Unity project before copying the new ones. This ensures that Unity does not retain any old references.
3. As you discovered, placing the files in a new folder can also trigger Unity to import them correctly, as it treats them as new assets.

These steps should help Unity recognize the updated files and load all textures correctly.

Vein Are you using SkeletonGraphic to instantiate the skeleton? If so, you need to enable Advanced - Multiple CanvasRenderers. For more details, please refer to the "Important Material Requirements" section of the SkeletonGraphic component in the spine-unity runtime documentation:
https://esotericsoftware.com/spine-unity-main-components#Important-Material-Requirements

Vein I see, in that case, manually reimporting as suggested by Spinebot may solve the issue.

Generally, updating via File Explorer as you tried should work. If that doesn't work, there may be an issue such as the .atlas.txt file not being updated or the correct file not being referenced. If manual reimporting doesn't work either, please open the .atlas.txt file in any text editor and confirm that it contains information about the second texture atlas page.
If that is correct, make sure that SkeletonDataAsset is referencing the correct atlas file in Unity.

@Vein There should be no additional steps like Reimport necessary at all after replacing your skeleton assets. While it does not really help, you could delete the old skeleton assets before copying the new ones over, but be sure to only delete the .skel.bytes or .json, .atlas.txt and .png files and not the actually referenced and potentially modified generated Unity assets like Material, SkeletonDataAsset and the like. In general the only reasonable files to delete are additional no longer needed atlas texture page .png files if the number of pages has gone down from e.g. 3 to 2 pages.

In general, all you need to do is just be sure that the previous existing skeleton asset files are overwritten by the new files, and that no duplicates are made because the file of the same name already exists.

If the issue reoccurs and can be reproduced, could you please create a minimal Unity project which still shows this issue? You can send it to contact@esotericsoftware.com, briefly mentioning this forum thread URL so that we know the context. If there is a bug, we would be happy to fix it.

Vein Glad it helped, thanks for getting back to us!