You cannot access the compressed root system from gparted, so i doubt that the system itself is corrupted. But you could corrupt the loaded kernel during a crash. The whole information on putting nitdroid on the N900 is very fragmented all over the net... Which how-to did you try to follow? Did you start gparted from an installed system or from Live-Media like CD, DVD or USB-stick?

Did you try to flash with both your batteries?
Which OS do you use on the PC you are trying to flash from?

Edit:You could have done damage to the second partition,but that would not stop the phone from booting, as far as i know. You just would miss lots of additional applications and your custom settings.