If the document is not yet in a Certified PDF workflow, choosing this option and running the preflight will start the Certified PDF Workflow. See Working with Certified PDF documents
A Certified PDF Preflight is always run on the complete document. When choosing Certified PDF Preflight, the page selecting options will be unavailable.
Enfocus PitStop Pro will run the Preflight on the selected pages, using the selected Preflight Profile.
After finishing, the Enfocus Navigator will show all errors, allow to restart the Preflight, suggest solutions, etc. See Using the Enfocus Navigator