I know that this isn't completely tested to see if it is a consistent behavior, but I ran into an issue after upgrading a Leopard server to Snow. The server was running mail services utilizing both the standard spool location and an alternate mail store.
After the upgrade all seemed to be well, but we shortly discovered that the users who used the alternate mail store didn't have access to their existing mail. The users in the standard location were just fine.
After poking around I saw that the alternate store contained two sets of user mail directories within the dovecot directory. One was named with the users shortname, ala Cyrus and the other used a GUID, ala Dovecot. Apparently during the upgrade the existing folders were converted to Dovecot format, yet new folders were also made. By renaming the folders with the shortnames to the GUID, proper functionality was restored to the users mailboxes.
It was a simple fix, but it took some poking to figure it out. Also being new to Dovecot it took me longer than it probably should have to resolve. Hopefully this will save someone else some time.