In Empathy, when you go to history, you have the option to delete all history and not for only a specific user.
How to delete the history of a specific user in Empathy people nearby account with preserving the history of other users?
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The logs from Empathy (using the telepathy library, hence the naming) are under
(Note that this is a hidden directory - use the terminal or
Show Hidden Files in Nautilus)
Logs are stored in this directory in the structure
Delete as appropriate.