I have been told that the "real" path is "/home/pi/PandaPI/Marlin2.x/pandapi/stm32f103cbt6.bin" but I do not understand why they look different. I have, however confirmed that this path exists and the bin file is there.
I was also told that "one jumper" needs to be installed in order to accomplish the MCU flashing, but I have not been able to guess which jumper that is.
It is, of course, essential to be able to reflash the MCU and the Pandapi can not be installed until that is confirmed. It would be really nice if it could be done with a bootloader instead of a hardware programmer.