Nothing is lost: open the merged file, drag the page thumbnails into the right sequence and save. That is faster than merging again, and it also handles a duplicate cover page or a stray landscape scan.
1Open the merged file in Organize PDF PagesEvery page appears as a thumbnail you can drag.
2Move the pages into placeDrag single pages or a selection. Deleting duplicates and blanks in the same pass saves a round trip.
3Rotate anything that is sideways while you are thereThe same view rotates pages, so the bundle comes out consistent.
4Save and check the seamsLook at the first page of each section: that is where a mis-ordered merge shows up.
Why does this happen?
File names sorted differently from how you think. File managers sort text, so page10 comes before page2. Zero-padded names (page02) sort correctly.
The selection order was not the list order. Ctrl-clicking files adds them in the order you clicked, which is rarely the order you meant.
A two-sided scan produced reversed backs. Flipping the stack means the backs come out last-to-first, so interleaving without reversing scrambles the document.
One source file was already out of order. The merge preserves each file’s internal order faithfully — including a mistake made earlier.
Questions
Do I have to merge again to fix the order?
No. Reordering the finished file copies pages within it and is quicker than repeating the merge.
How do I merge files in a specific order next time?
Add them all, then use the arrows in the file list before merging. The list order is the page order.
Does reordering re-compress the pages?
No. Pages are moved as they are, so scans keep their original quality.