It does look like the Adjustment layer is not being applies flatten fail the apply the adjustment. Even if converted into a Smart object layer. Yet the object open fine. Merge down also down did not apply the adjustment and even using a script did not apply the adjustment.
Photoshop 2020 the same CS6 the same
Could you please post a screenshot taken at View > 100% with the pertinent Panels (Toolbar, Layers, Channels, Options Bar, …) visible before and after flattening the image?
Its like the hue/saturation colorize checkbox is not being applied.
Did you check at View > 100%?
It look good at 100%. The chicken images is very poor when Photoshop Zoom am image the scaling is done quickly for performance. The scaled image quality fill size image. If I have the layered chicken psd omen in Photoshop and drag the flatten version as a new top layer and set the top layer blending to differences the should net no difference between layer and the chicken in the composite of the layer below the image should display 100% Black.. When It doe that it display 100% black. You would think the image would still display 100% black. Perhaps it would all the layers were canvas size and all layer scaled exactly the same way. However we have three pixels layer with different bounds. The poor quality chicken did not scale well at all the print and green scaled well. So I would expect the chicken colors to suffer during scaling
That seems to be a preview issue.
If you flatten the image with the Difference Layer does it turn completely black?