Message Store corrupted and backup restore won't get it back.

On March 31, my Acronis True Image 2015 made a backup of my entire computer. Windows Mail still worked. This morning, I got a message that the message store was corrupted, but Windows Mail was able to fix it. However, it isn't truly fixing it. It is leaving all the mail that I had already read marked as unread. It isn't putting the folders where they were originally. I have close to 8000 emails and 6000 of them have already been read. I can't go through them all again.

There are several folders that appeared in my Recycle Bin from the Windows Mail folder. They are dated April 3, 2015. This is likely when I last accessed my email. Restoring those folders back to where they belong didn't change things. I was still told the Message Store was corrupted and Windows Mail did the same thing.

So I pulled the Windows Mail folder from the backup of March 31 and copied it into the folder, yet the same thing is happening. What is preventing Windows Mail from seeing a good set of files and using them?

My next attempt is to use the "recovery" option in Acronis to put the files back, but hope is dwindling. Does Windows Mail make a note in some file somewhere that I also have to recover so that it doesn't think the Message Store is corrupt?

I didn't have time to wait. No matter what I did, Windows Mail repaired the message store so I let it and then spent the day moving files from the "Recovered" folders to my new folders. I'd still like to know why getting the message store file from my backup didn't allow Windows Mail to use the folders that I also restored from the backup.