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A scanner without a duplex feeder gives you two files: all the fronts in one and all the backs in the other. On their own neither reads properly. Interleaving them puts the document back together.
The backs usually come out in reverse order, because turning the stack over flips it. There is a setting for that, and it is on by default since it is the common case.
Put pages one to eight in the feeder face up. The scanner takes the fronts in order: one, three, five, seven. Now lift the stack out and turn it over to scan the other side.
The sheet now sitting on top is the one that was at the bottom. So the backs come through as eight, six, four, two, which is reverse order. Nothing has gone wrong. It is simply what happens when you flip a stack.
That is why the reverse setting is ticked by default. If your scanner or feeder already handles it, untick it and the pages are taken in the order they appear.
The PDF holding the front of each sheet.
The PDF holding the other side.
Leave it ticked unless your backs are already in order.
Save the woven file. Both originals are left untouched.
Add the file with the fronts, then the file with the backs. The pages are woven together one from each, and the new file is ready to download.
Because of how a stack behaves when you turn it over. Feed pages one to eight face up and the scanner takes one, three, five, seven. Turn the whole stack over and the sheet now on top is the one that was on the bottom, so the backs come out eight, six, four, two. The setting for this is ticked by default because it is what usually happens.
That is fine. Pages are taken in turn until one file runs out, then whatever is left over is added at the end.
Merging puts one whole file after the other. This takes one page from each in turn, which is what you need when the two files hold opposite sides of the same sheets.
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