Apparently they have "refined" the scope of the problem and it may be possible to use the scanners with Sierra without problems if you avoid certain workflows.
Of course my most frequently used one is scanning to Evernote from the ScanSnap App and this can cause a problem. Seems you can just save the document on the Mac and then drag into Evernote.
Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank.
Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder]
Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents* *No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.
Do not select the following functions in either Quick Menu or Application
[Scan to Print]
[Scan to Evernote (Document)]
[Scan to Evernote (Note)]
[Scan to Google Drive]