You're stitching three reports into one annual review. Each report has a careful bookmark outline — executive summary, methodology, findings, appendix. Lose those and your reader gets a 300-page wall of pages with no way to navigate.
Merging should respect that work. Here's how Flint handles bookmarks during a merge.
Why most merge tools destroy bookmarks
Cheap merge tools concatenate pages and call it done. They don't read the source documents' outline tree, so bookmarks disappear — every entry pointed to a page that no longer exists in the new file. The result looks intact but loses every chapter marker, every named section, every link a reader might have used to skip to page 240.
How Flint preserves the outlines
When you merge in Flint, each source file's bookmark tree is rebased onto its new page range and attached to the output. If file A had bookmarks for pages 1-50 and file B had bookmarks for pages 1-30, the merged file has bookmarks pointing at 1-50 (from A) and 51-80 (from B). The hierarchy survives. Open the bookmark sidebar in any reader and you'll see both trees, one under each source.
Add a parent bookmark per file
Flint optionally inserts a top-level bookmark named after each source file, so 'Q1 Report' and 'Q2 Report' become parent entries with their original outlines nested underneath. This is what you want for combined annual reviews, regulatory filings, or any document where readers need to know which section came from where.
When bookmarks won't survive
If your source PDFs have no bookmarks to begin with, the output won't have any either — Flint preserves outlines, it doesn't invent them. To add bookmarks to a bare PDF, edit it and add them manually. For source files exported from Word without 'Create bookmarks from headings' ticked, regenerate the export with that option enabled.
FAQ
Does this work with named destinations?
Yes. Named destinations and the outline entries pointing at them are remapped to the new page indices.
What about internal links between pages?
Internal hyperlinks (e.g. 'see page 47') are remapped if they live within the same source file. Cross-file links can't be preserved because they didn't exist before the merge.
Will the file size grow much?
Bookmarks add kilobytes, not megabytes. The merged file size is essentially the sum of the inputs.
Can I edit the bookmark tree after merging?
Yes, using edit PDF you can rename, reorder, or remove entries. Flint just gives you a sensible default.
Keep your navigation intact. Merge PDFs with bookmarks preserved.