Note: The credit for this explanation does not belongs to me. I got this few years ago and save on my notepad but I forget to give credit to the author. If you read this, please comment.
The conversation history you are seeing in outlook is nothing to do with your archiving. Implementing Lync/SfB along side Exchange is giving you that functionality. This is a users personal conversation history, that they can refer to and manage as they see fit – and yes it contributes to the size of their mailbox but it’s insignificant size.
An archiving server on the other hand, stores IM and conferencing data to SQL. Archiving is normally deployed if a company needs to meet regulatory requirements, or would like to archive IM data for a period of time for their own personal ‘safety net’ reasons. If a user deletes something from their personal conversation history (mailbox) it is not removed from the server side archiving.
Retention policies and configuration is used on the server side archiving to determine how long you would like to keep data in the store, and how often to purge said data etc.
Question: Are we duplicating data?
Answer: Yes, but for two very different reasons.
One is manageable by the end user, and exists for their use, reference and history purposes. The other managed by administrators and used as the ‘go to’ point regarding incidents etc. A user could send an abusive IM then delete it from his own history, the purpose of an archiving server nullifies his attempts at covering things up.
Mailbox impact is trivial regarding conversation history.