I am having this same issue, in both the Mac App Store version of Evernote and the Direct download installer version of Evernote, version:
Version 6.4 (452969 Direct)
The data in use was recently restored from a backup using CrashPlan when my laptop was replaced.
I have been searching for details on whether or not I can identify permissions on my Evernote data store, and in searching for what I expect to find in ~/Library/Application Support/Evernote, I found that the only data store seems to be in the location where the Mac App Store version of Evernote would keep data (~/Libra