I went through the Sierra 10.12.1 betas and installed the general release yesterday. I am using Evernote Version 6.9.2 (454159 App Store). My initial problem hasn't changed when scanning from my Fujitsu ScanSnap S1500M. I get a pop-up stating that Evernote can't be opened (note that it has opened) and asks whether I want to keep my scan. My problem is addressed directly at Fujitsu has recommended a couple of workarounds.
note: I will edit this posting to let you know if one of Fujitsu's recommendations to install the Evernote application directly from Evernote solves my problem. It would seem strange that both versions couldn't be synchronized. I have already been using Fujitsu's second workaround, "dragging" my scanned files directly to Evernote and have recently discovered that I can "right-click" on a file and choose "Add to Evernote" which opens Evernote and deposits the file. Being that all seems to work internally within Sierra 10.12.1 my problem clearly lies with the ScanSnap Manager software Version 3.2 L80.
note: Didn't try to install Evernote's direct version. On 10/14/2016 at 11:52 AM, Per4merKC said: to go into the settings for a scan, and "Add" Evernote as a NEW application. That's all I needed since I don't "process" my PDFs and simply add keywords into the documents title.
I have a simple workflow in that I scan documents to a folder on my NAS and send them to Evernote. I was encouraged to read a comment on DocumentSnap that "Sierra 10.12.1...release notes...'Improves compatibility with Fujitsu’s ScanSnap scanning software.'...It looks as if both sides had work to do in resolving the issue." I have not independently verified this information but there may be hope for others experiencing different problems.