Well, there are times, when you want to get rid of some individual messages on Skype, while keeping other chat history. That's where the Clear history button really wont be the right tool.
Fortunatelly, all the history of your chats is saved in the file main.db which is located in your skype profile folder. That is something like C:\Users\[your windows username]\AppData\Roaming\Skype\[your skype username]\main.db
You simply download free tool SQLite Database Browser and open the file mentioned above with it (Skype has to be quit). Then you just click on tab 'Browse Data', select the table 'Messages' to view and search the column 'body_xml' for the message in question. When you find the message, then just edit it and save it. Do not delete the message! Otherwise the missing (deleted) message will be updated when synchronized again later.
This quick guide was inspired by this article. I'd like to thank to its author :o)