Just in case you haven’t already heard this – Do NOT put an OpsMgr Management Server or Root Management Server (RMS) into maintenance mode. It’s not supported, it’s ugly, and it may cause major problems in your OpsMgr environment. Microsoft realizes that it would be best to avoid this situation from occurring so it looks like they have moved to block Management Servers from being able to be put into maintenance mode (see http://windowspowered.wordpress.com/2011/09/09/management-server-maintenance-mode-in-scom-2012/). If you have put your RMS or MS server in Maintenance Mode, my personal recommendation would be to call Microsoft Support. They are best suited to handle this situation.
If that’s not the direction you are going to go, this is what we have compiled as a set of steps to resolve the issues which occur from putting an RMS into maintenance mode [Please note, Catapult and myself take no responsibility for impacts of this process in your environment – this was written just to gather what has been done by various OpsMgr administrators to resolve issues which occurred from putting an RMS into maintenance mode]:
1) Disable all Subscriptions [no reason to generate large amounts of non-actionable alerts while this process occurs]
2) Bring each of the OpsMgr Components out-of-MM.
3) Close all related alerts.
4) Shut down all services for OpsMgr on the RMS.
5) Shut down all services for OpsMgr on each MS.
6) Shut down all services for OpsMgr on each Gateway.
7) Rename the Health Service State folder to _OLD (C:\Program Files\System Center Operations Manager 2007\Health Service State) on the RMS, MS and Gateways.
8) Restart all services for OpsMgr on the RMS.
9) Restart all services for OpsMgr on the MS.
10) Restart all services for OpsMgr on the Gateway.
11) Validate the RMS, Management Servers and Gateways become Green again.
12) Resolve the associated Alerts.
13) Re-enable the disabled Subscriptions.
14) This can take some time to regain the OpsMgr health status again. Set a timer, wait and pray for good results.
Additional relevant links:
Forum discussion on this topic: http://social.technet.microsoft.com/Forums/en-US/operationsmanagergeneral/thread/b6aac68c-78ce-4510-921b-e1b8272d6e48/