This is an example of auto aperture related defocusing. As the lighting changes, the AE program nudges the aperture which results in defocusing the shot over the course of the time lapse. Because there is a big distance between the aperture values, and the AE program doesn't take into account what it did on the last shot, there is also a flickering which goes with this, and its so severe that SBG refuses to remove it because its outside the default adjustment threshold.

In particular pay attention to the flare on the sodium lights in the distance as well as the focus blur on the roof details. You can see the diameter increase as the shot becomes defocused as the iris opens.

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