Why the order goes wrong in a scan
A PDF is a list of pages, and a scanner adds a page to the list each time a sheet goes through. Anything that changes the order of the sheets changes the order of the pages. A stack put in with the last page on top comes out backwards. A sheet that jams and is scanned again ends up at the end of the file. A report scanned in chapters, because the stack was too thick for the feeder, ends up with the chapters in the order they were scanned rather than the order they belong in.
The order matters more than it seems. A contract, a lab report or an expense claim is read from the first page, page numbers printed on the paper are used when someone says to look at page 7, and a missing or misplaced page can make the whole file look unreliable. It is far easier to fix the order of the file than to scan the stack again.
Moving a few pages that are out of place
When only a few pages are wrong, drag each one to where it belongs. A page can also be moved a place at a time with its arrow buttons, or with the arrow keys when its grip has focus, which is handy for the last small adjustment. To move several pages at once, select them with a click and a Shift click, then use To start or To end. They keep their order among themselves.
The caption under each page shows its new position and where it was, like Page 3 (was 7). After a few moves it is the quickest way to check that the right pages ended up in the right places. If you move something by mistake, Undo takes the step back, and Reset returns to the order you opened.
A document that was scanned back to front
When the whole stack was scanned from the bottom up, the last page of the document comes first and the first page comes last. Reverse order fixes that in one press. Look at the first and last thumbnails afterwards. If the pages are now in order but the content looks upside down, the sheets were also turned, and you can turn the selected pages with the Left and Right buttons, or use rotate PDF for a whole file.
Reversing works on the whole list as it is now, so it can be combined with other steps, for example reversing first and then pulling a cover page back to the start.
Weaving odd and even scans together
A scanner that can only read one side of a sheet needs two passes for a double sided stack. In the first pass you scan the fronts, which are pages 1, 3, 5 and so on. Then you turn the stack over and scan the backs. The result is one file with all the fronts first and all the backs after them, and the backs are usually in reverse, because turning the whole stack over puts the last sheet on top.
Front and back scans weaves the two halves together. It takes the first half of the pages, rounded up, as the fronts and the rest as the backs, and builds front 1, back 1, front 2, back 2 and so on. If the backs came out last page first, leave Backs scanned last page first on. If you restacked the sheets so that the backs came out in the same order, choose the other option. A preview shows the new order before you apply it, for example 1, 12, 2, 11, 3, 10 for a stack of six sheets. It is one step, so Undo reverses it.
The helper assumes that the number of backs equals the number of fronts, or is one fewer. If the scanner skipped blank back sides, the two halves will not line up. Add a blank page among the backs where each skipped back belongs, then weave the scans.