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I have a strange effect on my model. I modeled the Portal Companion Cube and since there's a lot of similar objects, I created deep linked duplicates of them to make easy adjustments to all of them.

Since I wanted all objects on the same UV Map I use the TextureAtlas add-on to keep the separated objects but edit the UV all at once. But I noticed that half of the objects that I duplicated flipped their normals as soon as I pressed "StartManualUnwrap". Fixing the normals in that mode doesn't help since I assume what the Addon does is create a merged copy of the object, to the change doesn't translate back to the original.

What I don't get is why only half of the objects are inverted whereas the other half is just fine. AFAIK the deep link means the geometry exists only once and all instances link to it, so how can it be different?

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I also tried to unlink them all, but the effect remains. The only way to get gid of it is to merge all objects and fix the normals. But that way, I lose the option to bake all objects separately by mesh name in Substance Painter.

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    $\begingroup$ It's probably about inverted scale of some of those linked duplicates. If object with inverted scale gets joined with another one normals of one or another will be flipped. Try to use Mirror modifier instead as scale can't be applied to linked duplicates $\endgroup$ – Mr Zak Jul 26 '18 at 19:24
  • $\begingroup$ @MrZak Indeed that was it. They had negative scales. I duplicated my whole mesh for export and made all objects single-user. Then I could apply the scale and it worked fine. If you'll provide this as an answer I'll accept it. Thank you very much! :) $\endgroup$ – Michael Klement Jul 29 '18 at 7:19
  • $\begingroup$ I'd suggest you leave your own answer with details explaining how you solved the problem you had (some links to manual maybe as well to the corresponding tools you used), I won't answer. $\endgroup$ – Mr Zak Jul 29 '18 at 15:58
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So what fixed it for me was:

  1. Select all objects and duplicate them by pressing Shift + D.
  2. Make everything a single user object (hit U » Object & Data).
  3. Apply the scale and rotation with Ctrl+ A » Scale & Rotation.
  4. Go through each object with wrong normals and fix them (Tab to enter edit mode, select all by pressing A and then Ctrl + N to fix the normals)

When I then selected the Texture Atlas group and started the unwrapping everthing was fine, no flipped normals anymore.

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