How do I flush the query cache? How do I flush Craft's query cache so that I may query a relationship field again in the same web request with a new set of parameters? In this particular scenario, I need to handle it inside of a custom module so I need PHP and not Twig.

Yes, I am fully aware of cloning the original query in order to make a second query with modified parameters so do not mention that in your answer. It is not an option in this scenario and it does not answer my question.
Craft is using the default Yii queryCache component, which is set to the file system cache by default (i.e., what's in storage/runtime/cache.

There's no way to clear specific items in that cache, but you can clear all of it with Craft::$app-&gt;getCache()-&gt;flush().