What does PDF bookmarks mean for your PDF?
Bookmarks are stored as an outline structure, separate from the page content: a title, a destination and a nesting level. They are what makes a 300-page report usable.
They survive merging (each file can become an entry) and splitting (each part keeps the bookmarks that point inside it), and readers show them in a side panel.
A document with chapter bookmarks can also be split along them, giving one file per section, named after the bookmark.
Why do bookmarks vanish after you edit a PDF?
Because each bookmark points at a specific page object, and many editing operations create new ones. Delete a page, reorder a section or re-save through a tool that rebuilds the document, and the destinations point at pages that no longer exist — so the reader drops them rather than sending you somewhere wrong.
Tools differ in how much care they take. Some renumber destinations as pages move and keep the whole tree intact; others write the pages out and never look at the outline. It is worth checking the side panel after any edit to a document you rely on the bookmarks in.
If they have gone and the original is still around, the reliable route is to go back to it and redo the edit with a tool that preserves them, rather than rebuilding a hundred entries by hand.