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Isn't that just a measurement artefact? With a bandwidth of around 21 kHz (44.1 kHz sampling) the third harmonic will "disappear" once your fundamental gets above 7 kHz. There is also a small reduction just above 10 kHz. This could be where the second harmonic is outside the measuement bandwidth.
I've seen those same freq dependent steps on so many AP plots that it almost certainly is a measurement artifact. Further to this, suspected Vref artifacts could be interrogated on SE vs balanced OP's as there should be better CM cancellation on the bal OP.... depending on Bal -> SE circuit component tol.