Hi !
I am the maintainer of the Flarum package for YunoHost. It seems I only posted the relevant information on GitHub, and forgot about the forums. So yes, when upgrading the package extensions are lost.
Regarding performing the installation commands, my guess is that @Aristid was not using the correct PHP version neither the correct user. Currently the default PHP version shipped with YunoHost is 7.0, hence php points to php7.0, thus we get those errors.
cd /var/www/flarum
sudo -u flarum php7.3 composer.phar require fof/upload