I have not encountered the problem of flickering for more than six hours now. I removed the SSD drive connected by Thunderbolt to the Thunderbolt monitor. Furthermore, I set the Display to Generic RGB Profile and unchecked "Automatically adjust brightness."
In other words, I have eliminated everything that makes the Thunderbolt monitor special. It now works just like a plain vanilla $250 monitor. And it is weird that I am almost content and no longer angry at the incompetence of the Apple engineers that rushed out this fix that cost me a day of my life. (But then again: I am used to this kind of thing from my PC days.)
18:18: No, it did not fix it. It just happened again!
19:40 Just read this on the Apple discussion forum: "This turned out to be an "All-in-One" display cable or display electronics issue. The way I isolated it was to unplug the Thunderbolt connector of the All-in-One display cable from the computer (leave power connector to computer plugged in). I then plugged in a regular Thunderbolt cable between a Thunderbolt port on the computer and the empty Thunderbolt port on the display. In this configuration everything worked (as I had bypassed the Thunderbolt portion of the All-in-One cable). Everything plugged into the other display ports worked and the display sound and display video camera worked fine." So I did the same thing and connected the mac mini through the thunderbolt port (and bypassed the the built-in cable). So far, so good. I am holding my breath.
1. It is possible that the cable got damaged when I dealt with the failed update and moved the computer and monitor several times. Apparently, the built-in display cable has been an issue for a long time. (One might ask, of course, why the cable needs to be built in, in the first place.) But it is also possible that it is not the cable at all, but that it is a reversion to an old problem. See here.