Deep linking and multiple app instances

the accepted answer didn't work for me, here is what did:

intent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP);
startActivity(intent);
finish();

from the official doc:

If set, and the activity being launched is already running in the current task, then instead of launching a new instance of that activity, all of the other activities on top of it will be closed and this Intent will be delivered to the (now on top) old activity as a new Intent.

You need to do following things for your Activity in your Manifest.

android:launchMode="singleTask"

This tells the system to always launch the existing instance of the Activity if it is already created.

And you can handle the Intent then by overriding the method

onNewIntent 

See http://developer.android.com/guide/topics/manifest/activity-element.html for more information.

Well we had several issues with deeplinks. Like:

1. click on the same link twice only, first click triggered the correct view
2. opened multiple instances
3. Links in whatsapp or facebook opened a view in whatsapp itself because of their web browser.
4. on android 6 opened only one instance, but was only handling the first intent, second and third opens app but no action because the intentdata did not changed somehow.

So the following is not an clear answer to the question more an allround solution for several issues we had.

Our solution:

a) Created a new FragmentActivity

@Override
protected void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    setContentView(R.layout.activity_main2); //well can be anything some "loading screen"

    Intent intent = getIntent();
    String intentUrl = intent.getDataString();
    Intent newIntent = new Intent(this, MainActivity.class);
    newIntent.addFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
    newIntent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TASK);
    newIntent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP);
    newIntent.putExtra("intentUrl",intentUrl);
    newIntent.setAction(Long.toString(System.currentTimeMillis()));

    startActivity(newIntent);
    finish();
}

b) Manifest:

    <activity
        android:name="YOUR.NEW.FRAGMENT.ACTIVITY"
        android:label="@string/app_name"
        android:launchMode="singleTop">
        <intent-filter>
            <action android:name="android.intent.action.VIEW" />
            <category android:name="android.intent.category.DEFAULT" />
            <category android:name="android.intent.category.BROWSABLE" />

            <data android:scheme="http" />
            <data android:scheme="https" />
            <data android:scheme="scheme1" /> <!-- sheme1://-->
            <data android:host="yourdomain.com" />
            <data android:host="www.yourdomain.com" />
        </intent-filter>
    </activity>

c) handle the passed new intent in your activities onCreate() and onResume() by calling the following example function:

private void handleUrl(Intent i){
    String intentUrl = null;
    if (i != null) {
        intentUrl = i.getStringExtra("intentUrl");
        if (intentUrl == null){
            //hmm intent is damaged somehow
        } else {
            //because of onResume()
            if ( i.getBooleanExtra("used",false) ) {
                return;
            }
            i.putExtra("used", true);

           //DO SOMETHING WITH YOUR URL HERE
    }       
}