Hi Yasu,
I have looked for this kind of information, some time ago, on SAP website, to prepare a Delphix meeting with SAP experts.
I have got these information from a Landscape Virtualization Management document describing SAP system clone, copy and refresh...
You can describe this way what could be done in a clone configuration hook :
BDLS transaction execution, deactivate RFC destination, empty the message queues, redefine the users,empty the batchs waiting for execution , ...
I have some specific slides (part of them are in french but easy to translate ). I can share with you if you are interested in...
Cheers,
Marie