How can we quickly clean an existing environment to a state of fresh install...i

The safest way to proceed is to re-install and use a new primary data source.

yes ... however we want to make sure that the application does not refer to any existing content/rule etc, the reference of which might have been removed from the process models, however might have somehow skipped from the Application zip during export?

we basically want to import the application on clean Appian server (to simulate the behavior when the application will be imported on Production server)

Even better. A clean install will tell you whether your package contains everything or not.

There are other methods (e.g. deleting certain files + re-creating primary ds + running load.bat ) but they are not supported, so I wouldn't suggest going that route, just in case you hear about this method.