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There is an object shared between Blender scenes. So the same object appears more than one scenes (see below).
Is there a way to unlink the object from a specific scene? In my case I would like to remove the Cube.001 from Scene.001.

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There is Make Links - Object To Scene command and we can use it to add objects to another scene (see below). So I search for kind of an opposite action.

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While the active scene is Scene.001 select Cube.001 and press X. You can also right-click RMB on the object in the outliner and choose Delete.

Deleting an object only applies to the current scene, any other "copies" in other scenes will still remain there.

You can link the object back to Scene.001 by selecting it in Scene and pressing ⎈ CtrlL->Objects to Scene->Scene.001

You can also remove the object using python, you can type the following into blender's python console or paste it into blender's text editor and click run script. Changing unlink to link will let you replace the object back into Scene.001.

bpy.data.scenes['Scene.001'].objects.unlink(bpy.data.objects['Cube.001'])
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    $\begingroup$ blender 2.8. both objects from scene A and B deleted when delete object in scene A. $\endgroup$ – Albert Mar 14 '20 at 12:13
  • $\begingroup$ @Albert looking at 2.80,2.81,2.82 and a recent daily build I don't see that happening. Are you sure you are deleting the object? If you link a collection into a second scene and then delete the object from the collection in the first scene it will disappear from both scenes. $\endgroup$ – sambler Mar 20 '20 at 7:38
  • $\begingroup$ @sambler I'm having the same issue in a new 2.90.1 scene. I added my solution to this as an answer. $\endgroup$ – DAG Jun 10 at 19:22
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    $\begingroup$ @DAG When you create a new scene, you get some options, creating a linked scene produces the effect described. That is each linked scene uses the same object lists, so deleting in one also deletes in each linked scene. If you create a new scene or a full copy this does not happen. $\endgroup$ – sambler Jun 11 at 6:09
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You can simply delete the object, however per sambler's comment, linked scenes will delete the object from all scenes, thus:

On the scene and object to remove, do Relations > Make Single User > Object. Once this is done you can safely delete the object.

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bpy.data.objects.remove(bpy.context.scene.objects[id], do_unlink = True)

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    $\begingroup$ Could you elaborate more on this? How to use it, where to paste it? It could not be so clear for everybody. $\endgroup$ – cgslav Feb 25 '17 at 22:16
  • $\begingroup$ As far as I understood, you need to do that in Python, right? If so, place it at the point where you need it removed. Replace id with some identifier to actually get the object. If you need to do that manually, just delete button should work, doesn't it? $\endgroup$ – D. Skarn Feb 25 '17 at 23:41
  • $\begingroup$ I'm not OP of this question. Please add more information with Edit option. $\endgroup$ – cgslav Feb 25 '17 at 23:43
  • $\begingroup$ This will remove the object from every scene - the question specifically wants to delete it from only one scene. $\endgroup$ – sambler Feb 26 '17 at 5:22

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