NetApp also recommends that if deduplication is used on the source volume, then it should also be used on the destination volume. However, you are not restricted using deduplication on the source volume only.
The deduplication schedule is not tied to the qtree SnapMirror update. In other words, the deduplication process does not automatically start at the completion of the qtree SnapMirror transfer.
The fingerprint database and the change log files that are used in the deduplication process are located outside of the volume in the aggregate and are therefore not captured in Snapshot copies
http://www.netapp.com/us/media/tr-3505.pdf
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