You merged or rearranged a document, exported it, and the bookmarks that were in the original file are gone from the result. In PDF Arranger 1.14.0 this is partly a settings question and partly a known limitation with specific operations, and the official user manual is explicit about both. This guide covers the setting to switch on, the version requirement behind it, and the operations that can still cost you your outlines, with a workaround for each.
First: turn on Preserve document information
Open PDF Arranger’s Preferences and enable the option labelled “Preserve document information from the first file opened”. With that option on, and a new enough library underneath (see the next section), version 1.14.0 rebuilds the outlines of merged files when exporting, instead of discarding them. Two details in the wording matter: the information comes from the first file opened, so open the file whose bookmarks you care about first; and the option needs to be set before you export, not after.
Check the pikepdf requirement
Outline preservation requires pikepdf 8.0 or newer. The official Windows builds and the current Flathub package ship recent versions, so most users meet this automatically. The risk group is source installs and older distribution packages, where an older pikepdf may be present. If the Preferences option seems to have no effect, update PDF Arranger to 1.14.0 and, on Linux, work through our dependency guide to bring pikepdf up to date.
Operations that can still drop outlines and links
The official manual is upfront that, even with preservation enabled, outlines and internal links can be lost after certain operations. It names these cases:
- Changing the page size of pages that contain links.
- Generating or splitting a booklet.
- Merge pages (combining several pages onto one sheet).
- Hide margins.
- Overlay or underlay (pasting a page over or under another).
This is not a bug you can configure away; it reflects how much those operations rebuild the affected pages. Plan around it with the workarounds below.
Workarounds, operation by operation
- Page size changes: test on a copy first. If the resized result loses outlines you need, do the merge and reorder work (with preservation on) as your main export, and treat resizing as a separate job on a copy, accepting that the copy may not keep bookmarks.
- Booklet: booklets are normally produced for printing, where on-screen bookmarks rarely matter. Keep a separate, non-booklet export as your archival version with outlines intact.
- Merge pages, hide margins, overlay/underlay: apply these to the smallest possible part of the document, or as the final step on a copy. There is no outline editor inside PDF Arranger to re-add bookmarks afterwards, so keeping an untouched master file is the reliable protection.
- When bookmarks are the priority: limit the job to merge, split, reorder, rotate and delete operations, which are the page-level edits the preservation feature is built around, and verify the export in your reader’s outline panel before deleting any originals.
Our tutorials on merging PDF files and editing metadata cover the neighbouring settings if you are setting up a clean export workflow.
Still losing bookmarks on a plain merge?
If a straightforward merge with the Preferences option enabled, on 1.14.0 with pikepdf 8 or newer, still loses outlines, that is a case for the official GitHub Issues tracker. Describe which files went in, in which order, and which operation you used, and check first whether one of the operations above was part of your workflow.