How to Make Invisible Mail Messages Reappear

I'm just getting over a harddrive death. I had to send my harddrive to get scanned and just got back the files back yesterday. I ran into a strange problem.

Apple Mail was telling me that there were a number of unread messages in any number of folders. However, when I went to open these folders, no messages were showing up.

I had no idea what was going on so I hit Google. This led me to a bunch of posts discussing disappearing Mail messages. However, nothing in any of those posts worked for me.

I took out all the contents of ~/Library/Mail/ and put them in another folder. Then I opened up Mail, followed the instructions in the pop-up window, which repopulated ~/Library/Mail/. Then I again took out all of the contents of ~/Library/Mail/ and put them aside in a new folder. I then brought back all the original files and put them back into ~/Library/Mail/. I then reopened Mail (actually with the intent of taking screenshots of my problem to post online) and everything was working.

The only thing about this is is that this was not the first time I did that, and it didn't get fixed the other times. I can't figure out what I did differently so I can't explain why this worked now but not before.