This hint is inspired by and uses tricks introduced by the hint Repair Time Machine after logic board changes, and is used for a similar purpose. In this case, I used this hint to re-connect Time Machine after migrating a partition from one hard disk to another one. I know it works with an image copy of your partition.
DISCLAIMER: Do this at your own risk! Have a backup of at least your most important files on a separate medium! Do not attempt this if you are uncertain about any of the consequences or circumstances here! There are no guarantees that the following will work for you!
Start from a different disk if you want to copy the system partition (use the System DVD if necessary). In Disk Utility, select the target disk (which must have been partitioned so your Mac can actually boot from it!), click Restore, drag the target partition to the Target field, and the old partition to the Source field. Don't forget to select Erase Destination, or it will in fact just make a file copy. Progress will then be shown as copying blocks instead of copying files.
The copy will be almost identical to the original -- only the drive ID (UUID) will be different, and that is why Time Machine would try to make a complete backup if we didn't do something to prevent it. I have not tested whether a mere file copy of a partition can be re-connected successfully so that only incremental backups are made. It does seem to work with an image copy, though.
After the image is done, remove the old drive/partition, or otherwise disable it, so that you're not confused by its presence -- all commands that follow will refer only to the new partition, and a change will be made only to a folder in the Time Machine backup.
Important: First, disable Time Machine.
Next, open Disk Utility, select your new partition and press Command-I to display the partition's information. You will need the Universal Unique Identifier value; select it with the mouse, copy it, and paste it somewhere for use later. Then open Terminal and go to the last Time Machine snapshot:
$ cd /Volumes/my_backup/Backups.backupdb/my_mac/Latest
Replace /Volumes/my_backup with the full path to your (new) Time Machine drive/partition, and replace my_mac with the name of your Mac as shown on the Time Machine drive. This directory will hold one (or more) folders, each named after one of your drives or partitions. For safekeeping, display the old partition's UUID before you do anything else -- this is the one that Time Machine has attached to your backups:
$ sudo xattr -p com.apple.backupd.SnapshotVolumeUUID my_partition
Replace my_partition with the name of the partition that you'll be swapping the UUIDs on. The command will print out a UUID, just like the one displayed in Disk Utility above. If the UUIDs are identical (which they won't be, yet), Time Machine will make an incremental backup; If they don't match, it will back up the entire partition again.
$ sudo fsaclctl -p /Volumes/my_backup -d
Whatever you do, do not forget the matching command below to re-enable it again!
$ sudo fsaclctl -p /Volumes/my_backup -e
Now you can re-enable Time Machine, and it should recognize your new partition as the same as your old one, and only make an incremental backup. When the motherboard of your Mac has changed, proceed as described in the original Repair Time Machine after logic board changes hint.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20090213071015789