By "reinstall" you mean "update" using WAS console or wsadmin script, right?
Java specifications state a native library can't be loaded by two different classloaders in the same process.
In this case the class which makes JNI is being reloaded by a different classloader everytime you update or restart it, so the problem occurs.
One solution is to create a shared library with the JNI class, and the create a classloader for your app server and associate that shared library to it. This way, restarting your app won't make any change to the class loader in charge of your JNI class