If you do make something out of it, please be so kind and report.
Success!
To recap the problem: I loaded a channel settings to /tmp/enigma2/ for conversion by Blackhole Enigma 2 Import. The box started to reboot at random times, the small cogwheel in the upper right never stopped spinning, and I lost access to the GUI menu. The settings files did pass the Blackhole check, but were probably corrupt in some way. The XML did not display correctly in xed when I checked it later. I flashed 3 different images to the box using a USB thumbdrive, but this did not help at all.
Here's how the problem got sorted:
1.) Use Filezilla or another FTP client - I'm on Linux, but Filezilla works on Windows. PrismcubeManager seems to work under wine, too - to delete ALL files in these directories:
/usr/share/
/tmp/
/mtmp/
/config/
*** Some deletions were probably unnecessary, but the directories had files in them that looked related to bouquets and satellite data, so I deleted the entire contents of the folders. I had to do this a couple of times because the box rebooted and reconstructed the directories.
2.) After all the above directories were finally empty, telnet to the box and run "shutdown now".
3.) Put a thumbdrive with an update image (I used a Blackhole image that had not worked before) in the USB port.
4.) Power on the box and follow the instructions on the screen or LED display to flash from USB.
That's it. No need to use serial update if you have USB function, but it looks like USB flash update doesn't necessarily overwrite problem data. I still had channel data and network passwords, for example, stored after every USB flash. So i think it is necessary to make certain problem data is really gone.
Like I always say: "If you don't understand something, just delete it". :smirk:
Hope this helps someone!