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You donnt have to break your standby propogation for upgrading the EM.. In case of a multi-OMS environment, if the host on which you plan to install OMS12c is managed by a slb then you to have to provide Server Load Balancer (SLB) configured for your OMS 12c Release 1 (18.104.22.168.0) in the section - Identifying Host for Enterprise Manager Cloud Control
Then, enter the fully qualified name, and the secure and unsecure upload ports of the host where the SLB is running.
Once you provide these details the pre-upgarde console will pick them and use it to confiure the 12c agents.
I also wanted to let you know, that i have taken you feedback and we will update the upgrade guide to explicitly say what/how/why to do in HA upgrade usecase.
Thank you. Where can I find the most detailed documentation on this process? I have found some, but not nearly as detailed as I need to get this upgrade going.
Not sure what documentation you have looked at but there is a dedicated book on upgrade. It is always a good idea to check the doc library http://docs.oracle.com/cd/E24628_01/index.htm