OS 10.8.5 Apple Mail fails to find POP Mail folder in Library?

Six weeks ago I transferred my wife's Mail account from iBook 10.4 to new MacBook Pro OS 10.8.5 w/considerable difficulty and help from senior Apple advisor. Yesterday Mail showed a welcome screen and could not find its Library Mail folder. I've been working with an Apple Senior Advisor who is unable to solve the problem — anyone help?

We did a complete Restore using Time Machine but this issue remained Welcome to Mail. We opened that and set it up so we can get mail but it still will not find all ht extensive POP folders and m-boxes in the Hidden Library folder