Something went south in Mail.app’s handling of my mail. I was seeing really slow performance, inconsistencies in read/unread counts, and other weirdness. When I did my monthly clearout of my inbox — anything that had stayed in there unfiltered gets moved to an archive folder — and it seemed to bog down and rebuilding didn’t seem to take, I realized I had some problems.
Part of the problem is the “improvement” of individual emlx files over mbox files: good for indexing but non-standard. But as some have realized, these are all just text files. And even though there is no standard for mbox files, just conventions, a couple of people have made tools to convert piles of emlx into mbox files.
I ended up with my emlx files intact but no way to get Mail to acknowledge them.
In Mac OS X 10.4 “Tiger”, the default message format for Mail messages changed from the Apple custom mbox-package format to the new emlx format (where messages are stored in individual files for Spotlight indexing). However, if you need to recover from a hard drive crash, it’s almost impossible to recover your mail messages easily since Mail won’t import emlx files and you can’t add them to your mailboxes any other way.
This seems to be working just fine. I can only Leopard’s Mail is less-intransigent about how mail is stored.