Workflow that causes issue: I have a PDF book with multiple chapters. Each chapter starts as a PDF generated from InDesign with bookmarks (generated by a table contents) for the different sections in that chapter and a particular, chapter-specific page numbering scheme, e.g. the twelfth page of Section 2C becomes page "2C-12," the fifth page of section 3B becomes page "3B-5," etc. I start by combining all the chapter PDFs into a single full-document PDF. So far so good. The bug occurs when a chapter has been revised, a new chapter PDF has been generated from InDesign, and the pages from that chapter need to get swapped out in the full-document PDF. Irrespective of whether I use the "replace pages" option or if I first delete the old pages before inserting the new pages, the bookmarks and page numbering from the updated document fail to get imported with the new pages. Instead, the "old" bookmarks remain in the link tree in the Bookmarks sidebar, but when you click on them nothing happens. For the page numbers, what happens is the final page number from the preceding chapter gets applied to every inserted/replaced page.

Environment: Windows, InDesign 2024, Acrobat Pro v2024.003

Expected Result: I have found that I can achieve the expected result by using Bluebeam instead of Acrobat. The expected result is that when I replace the pages of a given chapter with all the pages from the updated chapter PDF, the bookmarks and page numbering for those pages will look the same as they do when I open the standalone PDF for that chapter.

Observed result: while Bluebeam has page replacement and page import dialog menus to allow importing the bookmarks and page numbers associated with the new pages from their updated PDF, Acrobat instead automatically tries to retain or merge the old bookmarks and page numbering scheme from the old or existing parts of the combined PDF in which I am operating, resulting in broken bookmarks and nonsensical page numbers.