What is the best practice for integrating legacy design patterns when there is a conflict?

Based on a previous question that suggests many applications that are developed without necessarily a thorough analysis of the different design patterns and systems that might be in conflict, or have not been designed to be modular enough to be extensible, there are many examples (typically seen in Microsoft and Windows applications) of visual design style inconsistencies.

If anyone has previous experience working on projects to resolve such conflicts, are there any general guidelines or best practices developed to deal with these situations?

Is it mostly solved from a development or design perspective? Are there other considerations that need to be weighed up? Or maybe just simply left as is because it is in the ‘too hard basket’?