I just realized that the chat log files are named not with the name of the one I chat with, but the one who initiates the chat!
This makes chat log files messy.
For example, if I start the chat, the file is named with my name, no matter with whom I chat. So if I chat with two people, the log file mixes the chat history of two people.
And it creates files like 'my name.html', 'my name (2).html' etc, which make things even more chaotic.

Another problem is on Skype itself. It doesn't allow to reallocate its chat history to some other location, but must be in %appdata%\Skype. If I reinstall the OS or restore my system to a previous state, the recent history is lost.