Hi.
Same question was asked 4 days ago. see here my answer: Reorder Encryted files (folder and order lost)
In short: Im afraid no. The vault structure can not be restored based on the files only.
You can try. More that “destroyed” is not possible. And as your vault structure is already destroyed, feel free to play around. Maybe a backup of the mess is still a good idea though. Just in case someone else has a better idea than me.