Here's what I've learned.
I had two BES servers sharing a config db. Mail system is Exchange and the database is SQL 2000. I backed up the config DB and stop BES services on both servers. I had the 4.1.0 install and the 4.1.4 SP. First, I upgraded the BES server that hosts the SQL server and config DB. Upgrade went fine. Once complete, I went ahead and applied SP4 to the 4.1 server. No problems there. After the last reboot after the SP4 upgrade, I waited for my Blackberry to receive or send email. Nothing was happening. Looked at the BES MMC and it didn't look like the BES was even scanning the Exchange mailboxes. Called Tech support and explained situation, as I was explaining what was going on mail started delivering. RIM Tech said it can take a few mminutes for the mailboxes to get rescanned. Anyway, at that point I had one working BES server. I started the upgrade on the second BES, using the 4.1.0 installed. When it encountered the remote Config DB the installer returned an error that the DB was pre 3.5 and could not be upgraded. After much looking on the blackberry site and the forums I found a KB that dealt with 4.1.2. Basically, it was either upgrade with the Full 4.1 with current SP or create an empty Temp config DB and point to the temp DB for the 4.1 upgrade and point to the real DB for the SP upgrade. I choose the temp DB option because I didn't have the full 4.1.4 install. I went through the setup again and made it past the DB section and the reboot section. After the reboot I had to enter in my CAL license, but when it made it to the SRP section the SRP info was blank (using an empty temp config db) and greyed out, so I couldn't edit it. At 11 PM and after being on hold waiting for RIM I decided to go home. I moved all my users from the BES that was down to the upgraded BES (benefits of two BESes with shared DB) and went home. This morning I got RIM on the phone and they got me the full 4.1.4 install. I removed all remanants of BES from the second server and installed using the full SP 4 version. Installed like a champ, although I did have to make sure I entered the old BES server name. Bottomline is I am running both BESes now on 4.1.4.
I think if I had only upgraded the first server to 4.1, then upgraded the second server to 4.1 before applying any service packs it would have been fine. I now have to upgrade my second pair of BES servers on the other domain to 4.1.4, of course this time I have the full install.
That's my story and I'm sticking with it.