We recently began moving mailboxes in bulk from 2003 to 2010 SP1 UR4(v1). Two users out of ~1200 reported missing custom Inbox subfolders they had created the morning after their mailbox was moved. One found her missing messages in her Deleted Items but the other hasn't found hers. I did some searching and stumbled across the UR4v2 threads. I called MS Enterprise Messaging Support to find out if these reports of lost messages in folders while moving were related to UR4, and after checking with his colleagues he advised this is not something they have seen and didn't think it was cause to delay moving the remainder of the mailboxes. We discussed the production interruption for upgrading UR4 to v2 and I was verbally told that there would not be any production interruption to update the patch, and the tech's e-mail which stated "This RU4 Update doesn’t require a restart . or We won’t have any downtime".
It interrupted client sessions on the CAS servers while I was upgrading the patch, luckily I only did one CAS at a time and it didn't need any reboots. Then our physical mailbox server took almost 4 HOURS to remove UR4, required a reboot, then it took 8 minutes to re-install, and another reboot, before we were online. The mailbox server isn't exactly a slouch either, with a pair of 6-core 2.4GHz CPU's & 24GB of RAM. Whomever is providing the information on this process to tech support is completely wrong and they took our entire email system down for half the business day.
I called MS back at 7:42PM (about 30 minutes before the uninstall eventually completed) local time and escalated to severity A and they said they'd call back within two standard hours. No callback on either number I gave them. This was COMPLETELY unacceptable. Thanks again for a quality product, Microsoft. Now it seems we'll need to export the remaining mailboxes to PST's for peace of mind before moving them.