Rembo's trick was easy and helps some, but I'm not sure how much good it really did for me. After an email meltdown yesterday, I attempted Time Machine recoveries three times of an Inbox from one email account and got nowhere. The box had nearly 10,000 emails, so I thought it had overwhelmed Time Machine, and instead imported the email files buried in the Library folder of an external clone of the hard disk. Cumbersome, but it got the missing emails.
Today I tried Rembo's trick and found that the "Time Machine" folder actually contained three folders -- one called Recovery, a second called INBOX and a third called INBOX-1. I used separate Smart Mailboxes to import all three, and found that the first one (from Recovery) recovered a few mails (making it look like a partial recovery I tried and abandoned), and the last two recovered the same large numbers of mails. But the second two recoveries pretty much matched those from the Import. Neither seems to have captured SENT mail although I asked for it in the second case.
Were the folders inside the Time Machine folder from the three different recovery attempts? This all seems a rather odd way to do things.