If it's saying invalid serial number after the update, try doing a system restore. Turn your H9 off and on again with the HotKnob and big wheel pressed. This will most likely help, but it will restore your H9 to your factory presets. You said you had your presets in H9 Control though, right?
Sorry to hear that you had so much trouble with the updating by the way. The H9 has generally speaking a much more bullet proof updating system than the earlier Factor pedals, but we have had sporadic problems where people need to fix the software responsible for the updating, i.e. the boot loader.