saving the file in default .docx and exporting it to pdf will preserve the same hierarchical bookmarks.
invoke (doc, 'SaveAs', fileSpec); - save the document in .docx.
invoke(doc,'ExportAsFixedFormat',pdf_filename,17,0,1,0,0,0,0,1,1,2,1) - export to pdf with bookmarks.
Hope this will be helpful to someone.