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random viewport clipping
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A colleague and I have both run into this problem in completely unrelated projects/scenes.
The behavior seems to be that any geometry below the z axis is clipped specifically in the top orthographic viewport. Even parts of a single mesh that sit below z=0 are not visible, but everything above the z axis is. I noticed that if I zoom out far enough all geometry reappears.
This occurred with viewport clipping turned off, but enabling it and adjusting clipping planes had no effect. I am having trouble reproducing this, it seems pretty random. For both my colleague and myself, the problem was resolved by merging geometry into a new scene.