Can you ssh in?
The DB can be backed up with:
sudo mysqldump -u root bookstack > bookstack.backup.sql
Files from the /var/www/bookstack dir:
tar -czvf bookstack-files-backup.tar.gz .env public/uploads storage/uploads
I have an alias for a full backup for my own instance:
alias backup='cd ~ && sudo mysqldump -u root bookstack > bookstack.backup.sql && sudo tar -czvf bookstack-files-backup.tar.gz --absolute-names /var/www/bookstack/.env /var/www/bookstack/public/uploads /var/www/bookstack/storage/uploads /var/www/bookstack/wkhtmltopdf ~/.bashrc /etc/php/7.2/apache2/php.ini'
Restore DB with:
sudo mysql -u root bookstack < bookstack.backup.sql
Restore Files with:
tar -xvzf bookstack-files-backup.tar.gz