Chat history files are "housed" on the computer where the IM chat took place. If the chat could have continued or occurred on a second computer, there is a possibility that while the chat history may have been deleted from one computer, the chat may have syncronized with the other computer and still be intact. You could try a call and chat logging third-party add-on to Skype such as NirSoft to see if it captured the conversation.
The rule is that when chat history is deleted -- it's gone.
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