From Fujitsu Support this morning:
You may add an application to the Application list in ScanSnap Manager. Right click again on the Scansnap manger and select Scan Button Settings then click on the Application tab, go down to the Add or Remove button and click on it. Click on Add, then the Browse button to select the path to your application (including the executable). Next go back to the Application Name box on the Application tab and type in the name of the application you selected and click O.K. and then close.
Picking up on this thread as I have the exact same issue.
Yes indeed, it solves the problem… until the next DevonThink update. Then the link is broken again and the configuration needs to be fixed as explained, each time.
Very annoying, particularly as it was working flawlessly for years until it got broken a few months ago, ironically when the enhanced configuration was introduced.
Would someone have a long-lasting fix for this?