Fujitsu’s ScanSnap announced a future fix in the works for their PDF creation tools on Sierra for Mac.
While this issue is manifested by changes resident in macOS Sierra with how certain PDF content is influenced when it is modified using the new OS, Fujitsu is working to resolve both ends of this issue. To start, Fujitsu will take the initial action to fix select applications that will allow ScanSnap to be used to create new PDF content going forward that is safe to modify on macOS Sierra. Then, Fujitsu will soon release a fix for existing PDF files created by ScanSnap. Until then, please do not use ScanSnap Organizer.
They seem pretty fired up to resolve this, which is good now that Apple is also pushing Sierra as a silent download for Mac users.