I've done a clean install of El Capitan. I do have a raw file back up of my home folder, containing the messages archive. This was created when I was in Yosemite.
I grabbed the entire contents of the Home folder (/Users/myusername). This includes the Messages folder in the Library (/Users/myusername/Library/Messages). This was just a direct copy to an external drive. This folder contains three files and a folder
chat.db chat.db-shm chat.db-wal [folder] Attachments
I've attempted to just copy these files from the external drive to the new messages folder on my hard drive, but the structure of new and old messages appears different and the direct copy did not restore my old messages.
I'm not sure what the content of the files is as they're not readily readable, but the new Messages folder in El Capitan has an Archive folder by default, which seems to contain the message content now, instead of whatever way it was being done in Yosemite.
Is there a way to recover the old messages using either the archive I have or iCloud?