Hmm. Okay...
EDIT: Open your History and select the events you wish to remove (by dragging, or by selecting individual events)
Right-click and select Delete Event (or for multiple events, Delete Selected Events)
If you want to disable your chat history on Linux:
Click the small Skype icon on the bottom right corner of the screen and select Options > Privacy
From the Keep chat history drop-down, select Disable History
Click Apply and Close
SOURCEIf that doesn't do it, you can remove your Skype profile (nukes entire profile)
In your terminal and with Skype not running....
create a backup
remove .Skype directory
logout / login or reboot