It totally depends on the combination of the hardware, the drivers and the software that handles the GUI environment (the so-called display manager) and finally the application software that is displaying stuff .
Each of these can (but not necessarily has to) force a re-draw (with the flicker) of the display.
Typically (in Windows) the first flicker happens when the display driver reconfigures the hardware for the new resolution.
In many cases the video-chip has to stop displaying. And then, 1 or more display-frames later, start producing output in the new format.
The monitor will see a brief disconnect/reconnect of the video-card and re-adjusts itself accordingly (see fooot's answer too).
In most cases the content of the display memory is not longer valid either, so that get's cleared too. Usually to a black screen.
Then in a second step Windows itself redraws all the display-components at the new resolution. As Windows doesn't know what is present in the display-buffer at this point (it has no way of knowing fur sure whether or not the video-driver blanked the video-buffer) this usually starts with a fresh blank screen in the default background color. Then Windows adds the task-bar, wall-paper, etc.
This may cause some more visual flicker.
And finally running applications may do an additional re-draw to re-adjust themselves to the new display size. (Especially if they are running maximized/full-screen or snapped to the borders of the display.)
To summarize: Some flicker is video-hardware related, some flicker is software redraw related.
Last but not least:
Some people are far more sensitive to this sort of thing than others.
It is sometimes (literally) "in the eye of the beholder".
Some people hardly notice, others find it irritating.