When performing an inplace upgrade, in cases where there are multiple domains in the source, the installer invokes upgrade tool even though the process is killed. This happens when it is invoked in GUI mode.
Install inplace in the CLI mode, and exit when the installer prompts you to select the upgrade tool at the end of installation process. This does not delete any of the domains present in the domains directory. Upgrade tool should be manually invoked from the bin directory.
When installing inplace in GUI mode, make a backup of the domains present in the domains root to prevent losing any domains in the process. At the end of the installation process, exit when the installer prompts you to invoke the upgrade tool. Copy any backed up domains into the domains directory if they have been lost. Launch upgrade tool manually to do an upgrade.