pdfToolbox can extract existing DPart Metadata or bookmark structures in a JSON format so that you can modify them and inject them back into the PDF document. 

This functionality is mainly used on the CLI with the --modifystructures parameter, but it is also possible to modify the structures within pdfToolbox Desktop. Here you need to create a Process Plan where you extract the DPart or Bookmark structures using Quick Check and import them using the "Apply Structures" Action.

1. Quick Check to extract the existing structure to JSON. Relevant Quick Check filter expression:
   - DPart: "$.aggregated.doc.dpartroot: true"
   - Bookmarks:  "$.aggregated.bookmarks: true"
2. "Apply structures" Action: JavaScript can be used to modify the existing structure from the Quick Check result and inject it into the PDF again.