For information Fail2ban read the files in alphabetical order in this folder. If you have a file jail-perso.conf and another zen.conf with identical parameter, zen.conf erase the jail-perso.conf parameter. You can use this to add parameters or erase yunohost parameters without hook.
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Good to know, however I like hooks to easily restore or install yunohost servers (including tons of config files everywhere).
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I use conf_regen hooks too but i use customs jails in /etc/fail2ban/jail.d before use them . I don’t write hook to replace them and I use /etc/yunohost/hooks.d/backup/99-conf_custom (and the restore file too) to save/restore them and many additionals files. Use conf_regen hooks to modify config file and backup hook 99-conf_custom to save all types of files is a great combination 
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Yes, I do the same. And a few days ago, I noticed this app that allows to add custom path/files to the backup without managing the hook ourselves.
I did not test it yet, but it may be quite handy.
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