When I open Mail in Lion, there are small differences in the number of messages in some mailboxes. For example, one folder has 1255 messages in Snow Leopard and 1200 messages in Lion. Considering the number of messages I have, it would be extremely tedious to go through all my emails to see which ones are missing In the Finder, the number of email files matches the number of emails that should be in a mailbox (1255 in my example), leading me to believe that the emails are not lost, but are simply not appearing in Mail. In Mail, if I select all messages in one mailbox and move them to a new mailbox, the "ghost" message files in the Finder seem to follow the "regular" email into the new mailbox folder (the new folder has 1255 files, while only having 1200 emails in Mail). Here is what I tried to get the missing email back (in order of increasing desperation and decreasing expectations): Export from Snow Leopard Mail to mbox files, import mboxes Leave the mail folder in place (Lion Mail upgrades it on first run) Rebuild mailboxes Delete the Envelope Index files Put all emlx files in a folder, add .mbox extension to folder, import Repair permissions Repair disk Any ideas? Edit: all the emails are "On My Mac", so it's not a problem with my email service. Edit 2: I verified all files within the mboxes are emlx files.