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To be specific, I have a shapefile on census block groups (CBGs) in Georgia, but I only want to use those in Atlanta's commuting zone (CZ).

However, commuting zone is not a field in the census shapefile, so I join the layer with a different table that links CBG IDs to CZs. If I want to filter this layer, I am prompted to define a virtual layer, which I duly do.

Yet when I save that virtual layer (showing all the original fields, and CZ, and only for CZ=141, which is Atlanta) the shapefile is empty, thus the geography is lost somewhere along the line.

What is the proper way to do this?

I am on QGIS 2.18.2.

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Instead of filtering the layer, make a Select By Attributes query, and when you go save it, mark the box that reads "Save only selected features".

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