How to stop a screen orientation change from resetting state in my application

Question

When my Thread starts, I set an AtomicBoolean to true. At the end, I reset it to false in the associated Handler.

When I change the screen orientation BEFORE the end of the Thread:

• onSaveInstanceState() prints that this bool is TRUE
• onPause() prints TRUE too. -> Logical

The thread ends, I change again the orientation:

• My Log.e "Bool" prints FALSE -> OK
• onSaveInstanceState() prints TRUE -> Problem
• onPause() prints TRUE -> Problem
• onCreate() prints TRUE -> Problem

OnCreate():

if (savedInstanceState != null) {
    boolLocThread.set(savedInstanceState.getBoolean("boolLocThread"));
    Log.i("APP", "load LOC: " + boolLocThread.get());
    if (boolLocThread.get()) {
       Log.i("APP", "show progressDialog again");
       progressDialog = ProgressDialog.show(App.this, "", "Loading...", true);              
    }
}

Handler:

Handler handlerLoc = new Handler() {
    @Override
    public void handleMessage(Message msg) {
        Log.i("APP", "Handler received (LOC)");
        Log.i("APP", "Suppress progressDialog (LOC)");
        progressDialog.dismiss();
        boolLocThread.set(false);
        Log.e("APP", "Bool: " + String.valueOf(boolLocThread.get()));

    }
};

OnSaveInstanceState:

protected void onSaveInstanceState(Bundle outState) {
    super.onSaveInstanceState(outState);
    outState.putBoolean("boolLocThread", boolLocThread.get());
    Log.i("APP", "save LOC: " + boolLocThread.get());           
}

In the OnStop method I set my boolean to false and in the OnPause method I dismiss my progressDialog IF it exists. If I don't turn the screen before the end, the bool is reset to FALSE, and there is no problem. How could I reset correctly my boolean? Thanks