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I managed to get my printer up and running again! Here is what I did:
Turns out that the error messages were misleading. No bad flash memory and no corrupted uSD!
The actual install process went through without any problems! With the 4.3.3 recovery image and with the 5.3 recovery image.
However: the problem here was that the installers always messed up the contents of the i2c Eeprom on the Olimex board.
As described in @gr5s guide, I had to run the command (for my UM3)
python3 /ulti_installer/configure_eeprom.py 9066
and then reboot the printer.
After that the operating system knows that is running on a Ultimaker 3 and everything is fine!
As (and this is also described by gr5) the software versions 5.x don't have the python script included in the images anymore you have to extract this from a older version. I copied mine from the 4.3.3 installation via SCP. Note that you have to activate "Developer Mode" on the printer in order to do this!
Interestingly, the Eeprom fix does not seem to be persistent with me: after installing 4.3.3 and running the python script the printer was ok. When updating to 4.3.97 it was broken again.. fixed it again and the upgraded to 5.3... broken again... and fixed it again.
Maybe the next update will break it again, so I will keep the serial cable in the Ultimaker draw, together with a USB stick containing the python script! 🐵
By the way: @gr5 , the download for the script on your website does not work. Maybe you want to fix that?