I just tested this and added new file to the /etc/apache2/sites-available directory in live web server(digital ocean container), then I deployed to the live server target. It deleted the file I added.
@Teodor, I ve read about your post and I was wondering if this is how it supposed to be? Every time I deploy docker container to the remote target on Digital Ocean, my web server files is defaulted, meaning that any file I added is getting deleted.