I restored from a snapshot i had and the problem is fixed, I still would love to know how to reinstall magento thought from bitnami because just removing the magento folder won't fix it since other services will still be running, perhaps I should use the uninstaller.
In any case
I installed all the patches mentioned above and the theme
unzip and then
sudo cp -r name_of_folder /opt/bitnami/apps/magento/htdocs/
once all folders are in place
I followed this tutorial
but done the command using the full path as mentioned above
sudo /opt/bitnami/apps/magento/htdocs/bin/magento-cli setup:upgrade
Just follow the tutorial and you'll be alright. This is how to install porto, next tutorial I'll teach you how to install Lisbon
If anyone knows how to quickly reinstall bitnami stack let me know.