It is in the nature of a partially sunny and partially cloudy timelapse to feature flickering and it could also be a desired effect. Despite playing the sequence slower (which may lead to a clunky animation) or using plugins like e.g. DEFlicker by RE:Vision Effects there is no way to get rid of it. I would have to render out, work on and process a much longer sequence with many in-between frames, which would make this timelapse quiet expensive.

If you are looking for a sky timelapse with no or extremely little flickering, check out my second one: Full April Day. Soon to be released on Blender Market!