This may be what you're looking for:
http://stefantsov.com/editing-skype-history-messages-database/
Basically it is showing that you have to use SQLite database browser and open the following file:
c:Users -WindowsUserName-Application DataSkype -SkypeUserName - main.db
c:\Users<UserName>\Application Data\Skype\<SkypeUserName>\main.db
From there you can edit what you need, delete individual messages and what not using the SQL language.