Checked against the current Windows build. Where an article names a menu, a button or a message, that is the wording in the application, not a paraphrase.
The order is the list, and the list is yours to change
The Merge panel is headed DOCUMENTS, IN ORDER and shows every document you have open, in the order they were opened. Select one and the arrow buttons beneath the list move it up or down; Add opens more files into the same list. Read the list top to bottom against the order you meant before you press Merge, because the result is that list and nothing else.
On the command line the order is the order of the arguments: creasepoint merge cover.pdf annexure-a.pdf annexure-b.pdf --out bundle.pdf. Be careful with a wildcard. The shell expands it and sorts the names as text, which puts part10.pdf ahead of part2.pdf and produces a bundle that is wrong in a way nobody notices until the recipient does. Write the names out, or pad the numbers to a fixed width when the files are created.
Check the joins, not that the file opened
Two places carry almost all the failures: the pages either side of each join, and the two ends. A merge that lost a page, took one too many, or put two documents the wrong way round opens perfectly well and looks fine from the file list.
The viewer draws the first forty pages, so a long bundle has to be checked in the saved file rather than in the panel. That limit is on what you can look at and not on what gets processed — whole-document operations still run over every page of the file. Pick the output location yourself, so the new file lands somewhere you will find it again and the originals stay where they were.
Bookmarks are carried across, and some of them are dropped
Merging builds a new document and imports pages into it, which on its own would leave everything hanging off the old document's catalog behind. That was measured here and repaired. Bookmarks are read from every input and remapped to the page each one landed on, attachments from every input are carried, and the title and author come from the first document, because several cannot be combined into one and taking the first invents nothing.
What cannot be remapped is stated rather than dropped quietly. A bookmark pointing at a page that is not in the result produces a note counting them — three of twelve bookmarks pointed at pages that are not in the result and were dropped. Where two documents give a form field the same name, that is one field with several boxes under the PDF specification, and the result says so. Read those notes. They are the only record of what the operation could not keep.
Number the pages after the pages are settled
Page numbers go in one of six positions — left, centre or right, at the top or the bottom — from a format string with tokens. {n} is the page number, {N} the page count, {date} today's date, and {n:000000} zero-pads, which is what a Bates stamp such as ABC-{n:000000} needs. A format with no {n} in it is refused, because a line that does not vary is a header and there is a Header tool for those.
{n} counts from the start value for the first page of the document rather than of the selection, so numbering pages 3 to 10 gives them 3 to 10. From a script: creasepoint number bundle.pdf --format "Page {n} of {N}" --position bottom-centre --out numbered.pdf. Two things to know before you run it. The text is standard Helvetica, which covers Latin script only, so a Devanagari header does not come out of this tool. And the number is written into the page's content, so it is part of the page from then on and comes off by deleting that object, not by pressing undo tomorrow morning.
A signature does not survive a merge
The application rewrites a document as a single revision, and a signature made over the earlier bytes cannot survive that. Merging is the operation most likely to destroy one, which is why the window shows a banner above the pages when the open document carries a signature, and why the command line reports the signature state of everything it has read.
So decide what the bundle is for. If it is going to a portal that will verify the signature on the annexure, merging is the wrong operation and the annexure travels separately. If the bundle is for reading, merge it and expect the signature to be gone. Signing with a DSC token covers signing the finished bundle instead, which is usually what was wanted in the first place.
The two places worth looking next.
Read the matching guide if you want the reasoning rather than the fix, and check limitations before spending any longer on it — some of what people look for here is absent on purpose.