Now, here’s what’s going to happen. Mail — despite the fact that it has already cached all your Gmail messages — will download all of them again. For me, with about 321,000 messages totaling over 4 GB, that took nearly two full days, even with a super-fast Internet connection. That’s an unreasonably long period of time, and a crazy waste of bandwidth since I already had copies of all those messages! Mail actually does this in stages, and I won’t bore you with the details, but I will say that at a certain point in the process, your ~/Library/Mail folder could be twice as large as it should be, or even larger. Unless you’re running critically low on disk space, don’t panic about that, because it’ll eventually settle down — but be aware that it could take Mail a very, very long time to purge all those duplicate messages and return your ~/Library/Mail folder to a reasonable size.
UPDATE: Apple has since addressed the issues by updating the Mail app for Mavericks.