In Bitnami stacks we've configured by default SFTP. Could you please follow our FAQs in GCE? That guide will point you to all the necessary commands to upload files to the server.
What is the purpose of removing the bitnami folder? The application has the htaccess configured so you should not be worried about that.
I hope this information is useful for you.
Thank you and best regards,
Was my answer helpful? Click on