Thank you for your advice. Unfortunately the printer isn't covered in warranty any more.
I would proceed in recovering the printer using the method described below, although I was hoping that more could be done over SSH.
I'll let some more time go by, maybe someone comes up with an idea or Ultimaker says something to this issue. All I did was upgrading the firmware and it already worked right after it, paired with the still working SSH connection this might present an interesting case to them as this should definitely not happen.