How to merge PDFs, and keep them in the right order

Merging PDFs is usually simple. When it goes wrong, the problem is almost always the order, or something lost without warning.

The ordering trap

Say you have scanned a twelve-page document as individual files:

page1.pdf page2.pdf page3.pdf ... page10.pdf page11.pdf page12.pdf

Sort those alphabetically and you get:

page1, page10, page11, page12, page2, page3, ...

This is not a bug. Alphabetical comparison looks at characters, and the character 1 sorts before 2, so page10 comes before page2. Every system that sorts by name does this unless it has been specifically taught not to.

The fix that always works is adding zeros: name files page01, page02, ... page12. Then alphabetical and number order are the same, and every tool gets it right. If you scan documents often, set your scanner to name files with the extra zero and the problem goes away for good.

The other fix is a tool that sorts by number, reading the numbers inside the names instead of the characters. ZIP to PDF does this when converting an archive, because zipped sets of scans run into this all the time.

Either way, check the order before merging. Reordering afterwards means starting again.

What happens to your files

How merging works tells you what survives.

Merging copies the pages of each document into a new one, in order. Page content (text, fonts, images, drawings) comes across unchanged. Text stays selectable. Nothing is redrawn or compressed again, so there is no quality loss.

Things that live *outside* the page content are less predictable:

Bookmarks. The bookmark list belongs to the document, not the pages. Some tools rebuild it and others drop it. Check this on a long merged document.

Links. Links to a page within the same file usually survive. Links to a page that was in a different source file may not, because that page has moved.

Form fields. These break most easily. Form fields belong to the document, and two merged documents may have fields with the same name, which clash. If you are merging fillable forms, test the result before relying on it.

Metadata. The merged file gets new document properties. Author and title from the sources do not automatically carry across.

File size

A merged PDF is roughly the sum of its parts, sometimes a little less.

It can be noticeably smaller when the same font or image appears in several source documents, because a good merge stores one shared copy instead of one per file. It can be a little larger because of the extra file structure.

If the result is too large to email, that is a separate job. Compress PDF reduces the size afterwards. Merging first and compressing once gives a better result than compressing each piece and then merging.

Merging things that are not PDFs

Often the job is to combine different kinds of files: a Word document, two spreadsheets, some photos and an existing PDF, all into one document.

There are two ways. Convert everything to PDF individually and then merge, which gives you control over each conversion's page setup. Or put everything in a .zip and convert the lot in one go with ZIP to PDF, which converts each supported file and merges the results in order.

The second is much quicker for a large batch, and it tells you which files it couldn't convert instead of leaving them out without a word.

After merging

Two things are usually worth doing to a newly merged document.

Add page numbers. A 60-page merged bundle with no numbers is hard to discuss. Page Numbers adds them. Do this *after* merging, because the numbers are drawn on permanently and reordering later would leave them wrong.

Check the joins. Look at the first page of each section. Mixed page sizes and orientations are the usual surprise. An A4 report with a landscape A3 drawing in the middle may be fine, but often nobody meant it.

A practical order of operations

For assembling a document from many pieces, this sequence causes the fewest problems:

1. Get every piece into PDF form.
2. Put them in order. If the files are sorted by name, add zeros to the numbers.
3. Merge.
4. Check the page order and the joins.
5. Add page numbers.
6. Compress if it needs to be emailed.
7. Protect it if it needs a password.

Each step needs the one before it to be finished. Doing them out of order means redoing work.

Checking the result without reading all of it

A merged document of 200 pages does not need proofreading. It needs three specific checks, which take about a minute.

The page count. Add up what you expected. If the number doesn't match, a file was missed or added twice. That is the most common merge mistake, and you won't see it unless you count.

The joins. Jump to the first page of each source document. A wrong order shows up there and nowhere else.

The last page. A document ending mid-sentence means a file was truncated or the wrong one was last.

Bookmarks, links and what happens to them

Two things behave differently, and both catch people out.

Links inside a document break. A contents entry in document A pointing to its own page 12 now points to page 12 of the merged file, which belongs to a different document. Nothing looks wrong, but the link goes somewhere unexpected.

Bookmarks may or may not survive. Depending on the tool, each source document's bookmarks are either kept under their own heading, merged into one flat list, or dropped. If your documents rely on bookmarks for navigation, check the merged file before assuming.

Neither is a reason not to merge. Just check anything with a table of contents in it once.

Merging things that are not PDFs yet

If half your material is Word documents and images, converting each one and then merging is the long way round.

Convert the odd ones out first (Word to PDF for documents, Image to PDF for photos), then merge everything in one go. Or, if it is a whole folder of mixed types, ZIP to PDF does the conversion and the joining together, ordered by filename.