I have Ubuntu and Windows installed on my old computer, and just for funsies I decided I would do two things:
1. Back up all my old documents on to an external harddrive.
2. Update Ubuntu to the latest distribution (9.04)
Unfortunately, I decided to update Ubuntu first. The update went fine, but when I rebooted my computer I couldn't boot up Windows. A startup file was missing. Turns out I left Windows in hibernation mode - bad idea. I started up Ubuntu to try and fix the problem from there, but Ubuntu won't let you access hibernated drives - or so it says.
I used the Windows recovery disk to fix the master boot record, but guess what that did? Now I couldn't boot Windows OR Ubuntu. I had to take out my trusty Super Grub Disk to repair the MBR. I was finally able to get back into Ubuntu, and it turns out you can enable access to hibernated disks.
Quick sidenote; it's absolutely asinine that you have to use the terminal to do anything useful in Ubuntu. This is why Linux is not catching on - everything should be accessible from a GUI. Also, if I'm the only user, I should have full privileges, I shouldn't need to be "root". There are all these levels of security that seem redundant and confusing.
Anyway, I somehow enable access to the harddisk and I'm able to drag the necessary file from the Windows CD on to the harddrive. So it only took about 4 hours, but thankfully I was able to update Ubuntu, back up my documents, and get full access back to Windows and Ubuntu.