Merging PDFs and what happens to bookmarks
Combining files is the easy part. What survives the merge is the outline, the links and the form fields, and each of them behaves differently.
What actually happens when two PDFs are merged?
The pages of the second document are appended to the first, and everything they refer to is copied across with them. Fonts, images and color profiles travel too, which is why a merged file is usually a little larger than its two inputs added together rather than exactly their sum.
The result is a new document. Neither input is modified, and the page order is the order you arranged the files in, so a file dropped in the wrong position is fixed before the merge rather than repaired after it.
Do bookmarks survive?
They do, when the tool copies the outline, and this one does: each document’s bookmarks come across and are re-pointed at their pages’ new positions. What no tool can invent is a top level, so merging three manuals gives you three outlines in sequence rather than one book in three parts.
If you want that top level, add it after merging. Renaming and re-nesting outline entries is a small separate job, and doing it once at the end is far less work than making three source documents agree in advance.
What about links and form fields?
Internal links follow their targets and keep working, and links to a web address are untouched. Form fields are the awkward case: two documents that each contain a field called “name” now contain two fields with that name, and most readers treat identically named fields as one, so typing in either fills both.
Decide before merging whether the fields still need to be fillable. If they do, rename them in one document first. If they do not, flatten the forms into fixed page content and the collision disappears along with them.
Why is the merged file larger than I expected?
Because each source brought its own copy of the fonts and images it used. Two documents set in the same typeface arrive carrying two embedded copies of it, and nothing about appending pages notices that they are identical.
Rewriting the file afterwards removes the duplicates and the unreferenced leftovers. That is worth a few percent on an ordinary text document and a great deal more on a merge of many small files, each of which brought a full font with it.
Where to go from here
Merge PDF arranges the files and combines them in one pass, editing the bookmarks is where the missing top level gets added, and organizing pages handles the reordering you notice afterwards.
Page ranges covers choosing the pages before you combine them, and PDF/A and long-term archiving explains why a merged file often wants rewriting before it is filed.