How Alternate & Mix two PDFs works
PDF Alternate Mix interleaves the pages of two PDF files in alternating order, A1, B1, A2, B2, …, so you get a single merged document that pairs each page from the first file with its counterpart from the second. This is exactly the operation you need after scanning double-sided documents on a single-sided scanner: one pass gives you the odd pages, a second (reversed) pass gives the even pages, and this tool stitches both stacks back together in the right sequence with pdf-lib.
A reverse option flips the second file before interleaving, which matches how duplex back faces come out. If the two PDFs differ in length, it interleaves up to the shorter one and appends the remaining pages, so nothing is lost. To split a PDF instead, or to reorder pages freely, see the PDF split and PDF page organiser tools.