@Thibaut ,
Don’t care about autoremove for now and try this
wget http://ftp.fr.debian.org/debian/pool/main/f/fail2ban/fail2ban_0.9.6-2_all.deb
dpkg -i --force-confmiss fail2ban_0.9.6-2_all.deb
mv /etc/fail2ban /etc/fail2ban.old2
dpkg -i --force-confmiss /var/cache/apt/archives/fail2ban*.deb
yunohost service regen-conf fail2ban --force
systemctl restart fail2ban
yunohost service status fail2ban
Edit @Thibaut
Then :
apt update && apt dist-upgrade
yunohost tools update
yunohost tools upgrade --ignore-apps
yunohost tools migrations migrate
/Edit
After, if all is gone well, you could do
apt-get autoremove && apt-get autoclean
But later, there is no urgency 
ppr