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VisIt isn't built to handle this case well. I don't know of an option or setting to fix or workaround this behavior. Perhaps another @visit-dav/visit-developers could chime in. But I think the key is to have the metadata provide information for all meshes at all timesteps. You could have an empty mesh at time 0. You'll have trouble if you try to render it at time 0, but that doesn't matter. Your issue with the mesh quality variable names should disappear.

Alternatively you could script things to create your own mesh quality variables automatically following a mesh naming scheme of your choosing.

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Answer selected by JustinPrivitera
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