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Yes, you should call ConvertPivotAnimationRecursive() with KFbxNode::eDESTINATION_SET as the first parameter, which means to convert from SourceSet to DestinationSet.
After you are done all this, it depends on you to reset source pivot or keep source pivot but set them to be reference. And you do not need to do so on per take, pivot is only related to nodes, not to takes.
Here is a brief documentation about pivot, for more details please check documentation of KFbxNode in 2011.2 SDK:
* A node has two pivot contexts defined by the EPivotSet enumeration. The node’s animation
* data can be converted from one pivot context to the other. Each context can be set to be
* either active or passive (reference). By default the two pivot contexts are passive. They
* need to be active to be processed during the evaluation of the node final transformation
* matrix. In its passive state, a pivot context can still be accessed to retrieve its content
* for any other required purpose.
Author: Jiayang Xu
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