Well, turned out it was something completely different. I just hooked up the board again and the panel due was blank. Suddenly everything stopped working.
It was also weird, that the Serial port changed. The working one was no. 4, the not working one was no.3. Then I thought ... wait a minute ... I've got two usb ports on my laptop, let's use the other one.
Turned out that connecting the duet to one port works, but connecting the duet to the other one doesn't.
I just used a usb tester. On the working port the duet board consumes about 300mA, on the non working port it consumes only 100mA.
And I thought the usb-port survied that 12V incident a couple of years ago. But even if the fuses seem to have recovered, that port is no longer able to deliver enough power.
So the entire problem all the time was having the duet connected to a broken usb-port which doesn't provide enough power.