It depends what's caused your clash.

If they are NTFS filesystems, then that's a bug in the NTFS filesystem
... not sure what Microsoft's bug tracker is for that.  It appears that
it only tries to avoid duplicate IDs in the same install, and doesn't
use the UUID standard for it -- we need to investigate this more.

If it's caused by you making a duplicate of a disk (with dd), and
leaving both disks in the system, then that's entirely your own fault :)
You can alter the UUID for the other partition with:

   tune2fs -U random /dev/hda9

The trouble with doing this ourselves is that we don't know there's no
other O/S on the system also relying on UUID mounting.

-- 
Duplicate UUIDs after Edgy update
https://launchpad.net/bugs/64909

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