Missing mail (that's still there)

Question

Recently a had my entire system throw a very strange wobbly, which messed up certain preferences and plists. And since my backup system has been down for a period of time i'm embarrassed to admit to i just had to grit my teeth and start fixing things.
Mostly it's been finding apps and areas of the system that have just had their prefs returned to default, but the oddest one so far has been mail, and i'm hoping that someone out there has a deep understanding of the way mail is stored and can help me out.
All of my emails in two of my POP accounts (and my main two accounts of course) which were dated before the big wobbly were still in the list, but if i trid to open or preview them it would tell me that they needed to be downloaded from the server. When i rebuilt the mailbox it simply lost all of the emails, so now i have nothing in the list prior to the date of the problem. BUT.. they're not gone! If i do a spotlight search for content that i know is in one of the missing emails it will find that email and display it, but of course the 'Show in Mail Viewer' link does nothing.
How can i find these mails and restore them?

Answer 1

Since you have converted from an earlier version of Mail, you may have issues arising out of leftover files, and conversion to Tiger and Mail 2.x, but with the Envelope Index file, for sure.
I want you to read the article at the link below, and as needed, get back to me with some observations, before attempting any changes:
http://docs.info.apple.com/article.html?artnum=301315
This issue of leftover files applies not only to mailboxes you have previously created (which are in the Mailboxes folder the article mentioned) but will also apply to those mailboxes in account folders created prior to the upgrade to Tiger.
In a pre-conversion to Tiger mailbox, the only file that really mattered, in regard to message content, was the file "mbox". In a mailbox properly created and established in Tiger, the only thing that really matters is the folder named Messages.
Thus, if you are able to compare the size of both the mbox file and the Messages folder, at the time of conversion (a mailbox trying to have it both ways), and they are approximately the same size, then you can reasonably conclude everything was converted. There are some very minor exceptions to this comparative analysis, but it basically holds.
Once all leftover files are removed, then at the root level of the original Mail folder, locate the Envelope Index file, and delete it -- if more than one file has Envelope in the name, delete those as well.
Relaunch Mail, which will announce that it is ready to import your mailboxes -- allow this to continue, and in your case, it will really only be reindexing all your mailboxes, and not importing any.
This will refresh this all-encompassing index file, and I think the the search for reply messages will be resolved.
There are numerous topics about issues surrounding conversion of mailboxes to Tiger and Mail 2.x, from earlier versions. One of them -- the lengthy topic at the link below -- may also be of assistance, and deals with the Envelope Index to some extent:
http://discussions.apple.com/thread.jspa?threadID=413196
This topic is particularly relevant if the mailboxes were large, and complex while used in 10.3 and Mail 1.3. It may not be very relevant, if you were initially satisfied with the conversion of messages, and did think any were missing, at the time you first upgraded to Tiger.
Let me know any questions. Post back here for specific instructions, and help after you have thoroughly investigated your Mail folder, and mailboxes, and the degree of conversion that may, or may not have been completed.
Ernie