I also had the problem where Scannable was suddenly putting my scans in "first notebook". I logged out of Evernote from the Scannable app and then logged back in and it fixed it. Then I had to go to recents and save the scan to Evernote again.
It is alarming that there is no notification that the two became disconnected. You have to be aware when you "save" your scan that it doesn't say "first notebook". I have LOVED scannable but I may need to find a more reliable alternative.