We recently applied CR1 to IC6.0 for a non-Production environment.
The installation of the updated Applications (EARs) went through successfully, but some post installation steps failed.
After that, the installer "rolled back". IBM Installer Dev team explained what happens:
"If a CR upgrade fails, it will rollback to the last successful installation, only when there is no xml schema change in the CR.
So if the installation history is 6.0GA + 6.0CR1, and CR1 install fails, it will rollback to Connections applications of 6.0 GA level.
However, the rollback has a side effect - that is, if there are some websphere server parameters changed between 6.0GA and 6.0CR1, such as jvm heap size, logging and trace setting, etc, those changes will be reset to the default settings."
Request for the CR install process to have a flag you can pass to Installation Manager, which when enabled would result in the rollback not occurring if the application (i.e. EARs) update process completes OK.