An APM Enterprise Manager (EM) custom install using an existing EM installation directory i.e. Upgrade mode, may have unintended consequences because the existing installed set of components will be completely replaced by the new selection.
Adding components or running database modification activities on an existing Enterprise Manager installation.
Running an APM Enterprise Manager (EM) custom install using an existing EM installation directory means that the Installer will go into Upgrade mode because it recognises the presence of the existing installation. This means that:
In general if running a custom installation it is always best to use a new/separate installation directory to avoid these unintended consequences.