The challenge: 

Dedicate hardware in VMWare to all SCOM servers and bring back fully functional all with no alerts from maintenance.

The technique:

Fail DB clustered resources to node2 which will remain up.  Place Node1 in maintenance mode.  Down Node1.  Dedicate hardware.  Start Node1.  Make sure all is well, stop maintenance mode for Node1.

Fail DB clustered resources to node1.  Place node2 in maintenance mode.  Down Node2, dedicate hardware.  Restart Node2.  make sure all is well, test fail-over.  Stop maintenance mode for node2.

Place secondary management server and any 3rd party component servers in maintenance mode.  Down servers.  Deicate hardware, then restart servers.  Make sure all is well.  Stop maintenance mode for these servers.

Place Root Management server in maintenance mode (you read that correctly), please note the server had a snapshot taken and is SP1...  Down RMS, and dedicate hardware.  Restart RMS.  Make sure all is well.  Stop maintenance mode.

Result:  Mission accomplished, Brad rocks!

Read the complete post at http://owsug.ca/blogs/brad/archive/2008/07/15/Hot-shot-OpsMgr-maintenance-_2D00_-No-alerts.aspx