To falsify an account of an event, often a financial one.
The Canadian Liberal government has a lot of expertise in cooking the books.
This phrase originated in the mid 17th century and relates to the act of cooking, where ingredients are changed, altered and improved by the process. Financial statements can also be so modified to the benefit of the cook.
Alternative: Such a change, in a negative way, is also seen in the expression to cook someone's goose, thereby depriving the owner of the benefit of the animal, either alive or dead.