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These commands, issued in a page with a quarterly frequency,
result in a graph in which both series are graphed at their native frequency (the default). However these commands:
result in both series being graphed at a quarterly frequency. Is there any way to apply a function like this to a linked object and have it graphed at its native frequency?

No, once you've performed a transformation at a different frequency, the "native" frequency becomes the frequency at which the transformation was performed.