If desktop chrome is running and I launch portable chrome via portable apps, after I close the portable chrome portable apps still thinks that portable chrome is running until I close desktop chrome, preventing me from "safely" removing the flash drive.
The portable version should be configured not to permit running a second instance by default. It should show an error that Chrome is already running. If you disable that via the INI file, you must close all copies of Chrome for the portable launcher to shut down.
Sometimes, the impossible can become possible, if you're awesome!