What does PDF bookmarks mean for your PDF?
Bookmarks are kept apart from the pages. Each one is a title, a place to jump to, and a level in the tree. They’re what make a 300-page report something you can actually find your way around.
They survive merging, where each file can become its own entry, and splitting, where each part keeps the bookmarks that point to its pages. Readers show them in a side panel.
If a document has a bookmark for each chapter, you can also split it along them and get one file per section, each named after its bookmark.
Why do bookmarks vanish after you edit a PDF?
Each bookmark points at one particular page, and lots of edits replace pages with new ones. Delete a page, move a section, or re-save through a tool that rebuilds the document, and the bookmarks end up pointing at pages that no longer exist. Rather than send you somewhere wrong, the reader just drops them.
Tools vary a lot here. Some update the bookmarks as pages move and keep the whole tree. Others write the pages out and never look at the bookmarks at all. If you rely on the bookmarks in a document, check the side panel after every edit.
If they’re gone and you still have the original, go back to it and redo the edit with a tool that keeps them. That’s far quicker than rebuilding a hundred entries by hand.