Since the update to MobileMe Mail, at any point during the day, whether I am receiving new mail, or moving mail from the Inbox to hierarchical folders, I've sporadically gotten an error saying Apple Mail needs to "repair its information", then forcing me to quit. This has happened practically every day over the last week-plus.
When trying to reopen Mail, I get a note saying I need to reimport all my messages, which takes about 20 minutes, and then, all should be well.
So far, as much as I can tell, no messages have been lost. But some of the metadata is definitely awry, as old folders long left untouched show that messages sent several years ago are now marked as having gone out today, with the timestamp of when my index was rebuilt.
Over the years, I've rolled up a lot of messages, and my e-mail archive is a great resource for me to find old conversations with family members (going back to 1996), or searching keywords to find the first time something came to my attention. My e-mail folder with my father, for example, has more than 3,100 messages in it. My "Blog" top level folder has 3,600 messages, "Commerce" has 3,200, "Comments" another 3,000. There are about 2,500 in the folder for messages to and from Mom, and between 2,000 and 4,000 apiece for Twitter and FriendFeed.
There's no question that alerts from the social services I use have accelerated my e-mail glut, and I'm a pack rat when it comes to saving my mail. But now that I'm starting to see more failures on my Apple Mail, which has been rock solid for more than a decade, I'm starting to "think different" about saving everything. I just might backup again and then go on a deleting run. Hopefully, I can get this solved before it's too late and I lose anything significant.