Thanks for the pointers, I'll work on a bootloader solution if there is no way to update the sketch via the serial connection and USB to Serial converter. The bootloader is not the root cause, it is the application. So if I can just reload the Blink sketch for example, it should revive the board.
If this was a standard board, I could just hook to the serial pins and reload the application using the USB FTDI Basic adapter. Are there "pins" for the primary serial / is it possible to load a sketch onto the Leonardo this way?