Thank you for taking the time to let us know the issue you had when upgrading the application. We could reproduce the issue so we've just opened a task on our side and we will work on debugging and improving the Bitnami configuration to not to run into this issue in the future.
Meanwhile, you can follow our process to migrate the data of your Magento site to a new Bitnami instance, that way, you can launch new Magento instances and export the data of your old installation.
Sorry but I don't fully understand your question, could you please clarify it?
Please note that we update Magento and all the base components that Magento needs to work in every release, so in case there is newer versions of PHP, MySQL or Apache, we will update them when releasing the latest version of the application. In case those versions include security fixes for some vulnerabilities, you will need to follow the migration approach that I shared above to secure your application.
Let us know if you have any questions.