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You can keep your current structure and import your AD structure in parrallele to it.
When you do the import, select create duplicate machines.
Start assining your policies to your AD structure and then you can start deleeting systems from your old tree. The deleeted machines from your old tree will then start reporting under the duplicate entries under your AD synch structure.
Keep on deleeting machines until they are all in your new AD structure. If you have policie problems you can always easily move them back to the old group.
Be carefull with the inactive agent maintenancew task though.