The package manager removes components that depend on components that depend on virtual parent components.
In the attached example project componentA depends on componentB.subcomponentA. componentB.subcomponentA depends on componentB which is virtual.
Build the attached example with
Start Python 2 SimpleHTTPServer with
Run the installer and install only componentA. Run the maintenance tool in package manager mode, add componentC and restart the maintenance tool. componentA is removed.