Citrix released a hotfix that corrects the issue I reported in part 1.
http://support.citrix.com/article/CTX128591
BUG 27692 Upgrading a Citrix Provisioning Services 5.6 server to Citrix Provisioning Services 5.6 Service Pack 1 causes all the target devices to failover to the new 5.6 Service Pack 1 server.
I’m testing the hotfix in the lab later today.