Download and install the updated version of CaptureOnTouch from the website.

The phenomenon
Regardless of the scanner settings being used, after scanning a batch of documents, to the left of the CaptureOnTouch screen will be a preview of what has just been scanned. To the right of the CaptureOnTouch screen, you are prompted to either "Continue scanning" or "Continue to next step". If you click on the left arrow and preview the document that has just been scanned, then scan a subsequent batch of documents and add this batch to the previous file by clicking on "Continue scanning", you will lose the pages of this subsequent batch in an amount equal to the number of pages you scrolled back to preview in the immediately preceding batch of scanned documents.

For example:
You scan a 5 page document, then preview this document by scrolling back to page 1. This means that you have scrolled back 4 pages. You then scan a second 5 page document by clicking on "Continue Scanning" and thereby add this document to the file with the first 5 page document you just scanned. Upon completion of scanning the second 5 page document, you click on "Continue to Next Step" and the file is then saved to the path chosen. When opening the saved file, you will have lost the last 4 pages of the second scanned 5 page document. The file for the first and second 5 page documents, which should be comprised of 10 pages, is now comprised of 6 pages.