I had the same problem when my update failed and stopped. It had changed some stuff, but the firmware level was still listed as the original. I solved this by flashing the original level from Navifirm. After that, the update ran OK, without any interruption. I wish had some better news for you.
One of the first things I did after the update, was to mount the N9 memory as a Windows drive with Dokan SSHFS. So I now include that drive letter in my Windows backup. So if I have to flash again, I will at least have the data in the Windows backup, if all else on the N9 fails.