This is a post for anybody who comes across this difficult problem, reported by gptsync , shipped with rEFIt in its partition editor. The error is:
GPT partition of type 'Unknown' found, will not touch this disk.

This is what I got when I resized my linux partition using parted, resulting in the GPT and MBR partitions going out of sync. Now this is something rEFIt's gptsync should be able to solve fairly easily, but if you have a so called 'BIOS Boot Partition', a small partition created by grub2 (as shipped with Karmic), then you're in quite some trouble. The partition tables won't sync and you'll find yourself unable to boot your linux system.

It took me numerous hours to fix this issue. And now that the necessary package has been fixed, the solution is fairly simple:

- Grab an Ubuntu live CD and boot
- Install gptsync_0.13-10 or higher from *Debian* packages (Ubuntu doesn't ship it, and the original rEFIt doesn't have the fix (yet?). Download from packages.debian.org and install with dpkg --install
- Run gptsync on the affected disk
- Reinstall grub ( $ sudo grub-install /dev/sda )

More about the issue can be read here: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=545190 , note though that the issue was erroneously believed to be fixed in 0.13-4, for the actual fix you need at least 0.13-10 .

I hope this post saves someone from two days of headaches