Initially the DB was created on Windows 7, FTPed to Azure (Windows Server 2012 instance), ran there for a few weeks and now FTPed back to my computer with Windows 7. It is on this computer that this database now just doesn't want to work. RavenDB version is 2360 on both sides (well it's embedded so I guess that's kinda obvious).
I always wondered how to manually shutdown the Embedded instance. I usually just shutdown the IIS website, wait a few seconds and then copy it. I do this a lot and while sometimes Filezilla will say that Raven files are still locked, most of the time copying would work (if not the first time, it would on retry).
In this latest case the copy completes successfully but obviously something is wrong with the copied DB.