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I have a test case taken from another model:

  • white_mesh is a digitized mesh, it works properly with booleans;

  • white_mesh_scaled is an empty mesh unioned with white_mesh; it works properly with booleans if a fast modifier is used (looks like a bug in exact if one of the arguments is empty, but it is not the subject of this question);

  • black_mesh uses Instance on Points in order to copy and move white_mesh_scaled.

Here is the problem: Point instance has been obsoleted in Blender 3. Because black_mesh did not work properly with booleans in Blender 3 (it did work in Blender 2.93), I replaced the obsoleted node with the new Instance on Points in a hope of fixing that:

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The resulting mesh black_mesh looks ok but it also does not work with some booleans anymore. In particular, its modifier Difference with black_cut_side does not change anything.

Of course, the problem may be outside of geometry nodes, because Blender's version changed. Anyway, how to correct for that?

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Add Realize Instances node before Output ...

enter image description here

... you can also use Mesh Boolean node instead of modifier.

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