Maybe this is not the answer you are looking for, but it is easier to monitor those changes instead of somehow forcing the update of the MediaStore, you can even apply this approach for when it detects changes to make your query again.
You need FileObserver to monitoring file changes, but first your need setup it, let me explain.
You need to create a BroadcastReceiver, which tells you when the device starts. Why? Because you need to know when the device starts to start monitoring changes to your files.
Then you need create one service that observe changes, the class that can help you are FileObserver, SingleFileObserver.
But that is general, you can see the solution in this answer in similar question.
How to monitor folder for file changes in background?