chat log are only stored locally.
i would suggest,
disable messenger chat logs (tools > options > messages > automatically keep a history of my conversations)
enable plus! chat logs (plus! > preferences > conversations > chat logging) and put a password on them (plus! > preferences > conversations > logs encryption)
see
Encrypting, decrypting etc. of Plus! chatlogs for details on how to encyrpt old plus chat logs.
to delete messenger logs go to My Documents\My Received Files\'your email'\History and delete the logs you don't want
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