As written in an earlier article, I experienced that Duplicate Items was removed by default when moving/importing/exporting mailboxes.
With the release of Update Rollup 2, Microsoft made it possible to specify whether Duplicate Items should be deleted or not, which I think is great news. I do still believe that default behaviour should be that nothing is deleted, but at least it is now possible to control it.
Please see KB875990 for detailed info.
~Christian
