Another possibility I thought of:

You could try creating a bootable CD that will start up a gparted(linux) session on your pc. This will let you see all hard disks connected, including all your n900s partitions. There is an option in there to click on a partition and check for errors/fix it. Once done just take the CD out and reboot to start the PC normally. With any luck any error on the disk might have been fixed and then flashing will work.

I used a gparted CD to repartition MyDocs and /Home
Will try and find all the info and where I ggot it from if you can't find it.