Well, the problem with the flickering Thunderbolt display has been solved. Bypassing the built-in display cable did the trick. I will try to find out how much it costs to replace the cable, but even if it turns out to be too expensive for me to fix it, I hope that the monitor will last another year or two. Given how much it cost (about $1000.00), it needs to last at least another three years. One thing has not changed: I can no longer connect to other Thunderbolt devices. Trying to put the monitor in second place of the daisy chain (and after the SSD drive) does not work). So, I will have to do without Thunderbolt for now. But, as I said, USB 3 is pretty fast.
There appear to have been four issues. First and foremost is the recent security update that broke the Thunderbolt connectivity. As I now know, it affected people who had a third-party SSD drive at the time of the update. I obviously don't know how many people those were and whether it affected only some or all of those people, but I do know that it affected me in the worst way, stealing at least two full days from my life. I understand that Apple couldn't care less about people who did not buy all of their overpriced peripherals but tried to save some money and better performance.
Secondly, the built-in cable which seems to be the weak link in the Thunderbolt Monitor—many of them don't seem to work right out of the box—got broken as a result of my moving the Mac Mini several (many?) times during my attempts at recovering from the failed installation. Ultimately I did recover, but don't ask me what actually did the trick. It were problems like this that ultimately made me move from the PC to the Mac. There probably is no way back to Windows without Parallels, and I don't like LINUX, so I am stuck.
Thirdly, I did not have a well-conceived backup plan but relied exclusively on Time Machine. Whatever else you do, re-think your own strategy.
And, fourthly, right after applying the security update (if not while the security update was going on), the Apple Applications Sore went down and did not get up again until more than twelve hours later.
This will be the last post on my present problems with Apple, but I will report, if the issues with the Thunderbolt connection get solved.
1. Since I talked so much about Apple's Thunderbolt Display, you might be interested enough to read this review. When I bought it in early 2012, it looked much better than it does now.