High harmonic spectroscopy gives access to molecular structure with Angström resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrödinger equation, either numerically or with the molecular strong-field approximation, we show that the electron dynamics in the emission process generally results in a strong spectral smoothing of the interferences, blurring the structural information. However we identify specific generation conditions where they are unaffected. These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy.