I, too, have this problem. I was able to solve it (I hope) by restoring folders from my latest backup, but I want to describe what happened in case it might be helpful to Apple or anyone else in understanding the problem or a fix. My Mail (v9.0) on my iMac links to two different earthlink addresses, one for me and one for my wife. Both accounts normally show, along with associated folders, in my Mail window. iCloud synch is not on for these, so this couldn't be a factor. All mail is (or was) on my iMac, except for a few recent ones on the earthlink server. My account (vs. my wife's) was probably the last account open before I upgraded. After the upgrade, my Sent folder was completely empty (it previously had >1500 emails in it), my inbox was empty except for brand new emails just pulled from the server (previously had about 10), and my trash was also empty. But the inbox, trash, and sent folders for my wife were all there and populated as they were before the migration. I see from other posts that others have lost subfolders, but I didn't. In fact, I didn't lose any of the folders I created myself (though I haven't checked to see if all have everything they should within; kind of afraid to look...), and no subfolders lost. So why such main and important folders (inbox, sent, trash) only? How could Apple miss that these might not migrate?
By the way, the unchecking and rechecking "enable this account" didn't fix it, and I didn't try taking anything from the library because the V2 list had a post-migration time on it and the V3 list had a 2012 date. Doesn't mean it wouldn't have worked; just afraid to try it and time machine seemed easier.
I would sure be interested in hearing from Apple how something this major could have slipped through and also how to ensure that everything, not just things we happened to notice are missing, has been restored/transferred properly.
Thanks!