Scanning a double-sided document with a scanner not supporting duplex (double-sided) scanning breaks the page order. To solve this problem, first scan the front and then the back pages with the document feeder. Next, select the PDF scan and let the app fix the page order.
Try out the app with two example PDF files: Example 1 and Example 2.
A project by Clemens S. Heithecker. View the source code on GitHub.