After you install Microsoft System Center 2012 Operations Manager (OpsMgr 2007) or System Center 2012 R2 Operations Manager (OpsMgr 2012), if you then use msiexec.exe to manually remove features such as the APM Agent or Operational Insights Agent (Advisor Agent), unexpected issues can occur.
For example, after doing this, when you import new management packs the configuration is never loaded successfully on management servers and agents. Additionally, the following issues may also occur:
Error 1209 events are logged in the Operations Manager log on all management servers.
"All Management Server Resource Pool is unavailable" alerts are displayed on the console.
This is just one example but others are possible. This is due to the fact that using msiexec.exe to remove these features is unsupported.