I had the same problem using Affinity with my CanoScan 9000F. My scanner simply didn't show up as a choice using Affinity, but did with Photoshop Elements.
After checking out manuals, posts (here, on the Canon Site, and on the Apple site), I called the tech support line for Canon. A very pleasant and knowledgeable technician explained that Apple is moving away from Twain to ICA. She suggested I disconnect the USB cable from my Mac, uninstall (see Canon manual) the ScanGear and restart the computer. It only took a few minutes, and my scanner showed up! I can easily scan now with Affinity. Perhaps you will have the same experience with your scanner. Good luck!