When remerging cyrus-imapd-2.1.11 all empty dirs in /var/spool/imap/* and /var/imap/* are removed, which causes cyrus to mallfunction! These dirs should perhaps be cfg protected so users emails aren't deleted by mistake if cyrus-imapd is unmerged?
If only the empty directories are removed, then it shouldn't remove anything harmful right? Also, if you re-merge while the server is running you WILL have problems... Please show me some log information if you would for further troubleshooting.
The problem is that cyrus expects these empty dirs to be there as it is there it puts it's data. If no dirs are there it won't start correctly. So if you stop the daemon, remerge (or update I expect) you will run into problems with the dirs that have yet to be populated with data. For me there is not really a problem right now as I just unmerged Cyrus completely and emerged it again (I had not yet set it up completely), but I dread updating after having had it running for a while.
cyrus-imapd-2.1.11-r1 is now in portage which keeps the /var/* directories.