Acrobat Preflight is indeed the tool you would need to use to map one or more colors to other colors. But due to the complexity of what you want/need to do, you would need to create a custom fixup based on color mapping/conversion. This is not a trivial task and there are no “step by step instructions” available for the process, the results of which might be all that visually satisfying anyway. The complexity is such that you may be best off editing the source document from which the PDF file was made and creating a new PDF file from that.
- Dov