Mail, password, super duper

Last week I lost my phone. My passwords were all pw-protected, but yesterday I observed some odd changes on my computer, so I changed my password. I had a typo in what was written down, so I had to use the OS X install disc this morning, and reset it.
When I opened Mail, it said my index was bad. I did a Safe Boot, and that appeared to fix the problem, but now I see that past emails are missing from my various mailboxes.
I use Super Duper, so theoretically I have a good version of everything from a couple of days ago, but when I launcehd, it did not show the dates of recent backups. I think that I only need to restore Mail, but at the moment I am apprehensive about doing anything.
Can anyone offer suggestions?
Thanks,
Nicky

Hi Nicky,
have you done the usual checks? Do you know applejack ? (applejack.sourceforge.net) this is a nice command-line routine which makes all standard checks in single-user modus. You can start your comp in single-user by pressing cmd+S when booting. After this your're prompted and solicited to do the fsck (file system check) and after a successful fsck to remount your disk in write modus.
If you have installed applejack, you can make this and more check routine (i.e. Permission repair, cache clearing, fix preferences). You have only to give this command line:
applejack AUTO restart
and applejack will check/repair the FS, fix permissions, clear caches, fix preferences, remove swap files.
If this is done and you have yet the problem, you must first save/backup your data for more action.
I hope this helps
Massimo

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