Emily opened her email 3 days ago and saw "Welcome to Mail".
That's bad. It meant OS X had lost track of her mail archives. The files were all on disk, but the OS knew nothing about them.
I didn't try entering new information of course. That would have been quite disastrous. Instead I poked around and found the usual advice to restore ~/Library/Preferences/com.apple.mail.plist from Time Machine. 
That did nothing.
Then I found Power loss, Mail accounts gone,...: Apple Support Communities, a post that recommended also restoring ~/Library/Mail/V2/MailData/Accounts.plist. That looked good, since her current file was 1kb and the old one was 6kb. After a Time Machine restore her email was back.
Of course this doesn't explain why her data was lost in the first place. HFS+ is supposed to be journaled, we should't lose these files even in a nasty crash. So now I have to run some drive diagnostics.
Update: . Oops, i should have read more closely damnit. I think the SuperUser article had the right advice pre-Lion.
Personally I wouldn't mess with /System unless the other two fail and the directory changed post Lion.