Regarding the "/usr/lib/jvm/jre/bitnami" directory, we were not able to locate such a directory in our Tomcat AMIs.
Note that independently of the system's JAVA_HOME value, the Bitnami installation should use the Java installation in "/opt/bitnami/java".
If that is not the case, it is probable the Tomcat scripts have been modified somehow. For instance, check "/opt/bitnami/apache-tomcat/bin/setenv.sh", as it should contain the following line explicitly: "JAVA_HOME=/opt/bitnami/java".
When the directory gets removed after upgrading, what is happening to your application? Is it not starting or are you not able to reproduce it due to the status check fail? Note that when you see the status check not working, it is more probable for it to happen because of SSH settings changes than Tomcat itself not working.
We recommend you checking SSH changes to ensure they are properly configured, and to ensure that SSH is configured to start when booting the VM. You can do this with "chroot" when you mount the volume and run "service", although you will need to mount some directories before for getting the commands to work (/run, /proc, /dev).