How to upgrade youtrack WAR?

What is the procedure to upgrade 5.2.1 to 5.2.3, if only the war was installed on tomcat?

We read the upgrade advice in your documentation - how ever, that wasn't unfortunately very helpful for our scenario ...

We tried:
1) Stop Tomcat
2) paste new war file in webapps directory
3) Start Tomcat
=> nothing happens - it stays with 5.2.1

1) Stop Tomcat
2) paste new war file in webapps directory
3) delete old youtrack directory
4) Start Tomcat
=> Youtrack starts up with the setup screen. If we click "Save" all settings and the issues are gone ...