Which form is correct: “having not done” or “not having done”?

Both are used.

It means Something has not been done, therefore…

For example,

• Not having finished her homework, she could not go out.
• Having not finished her homework, she could not go out.
• Not having been skiing for three years, I’m not sure I can remember how to do it.
• Having not seen the film, I can’t comment on it.