I have been using letsencrpt for several years now. The initial set-up worked well more or less from the first time.
However my git clone of letsencrypt client is outdated and I would prefer to replace it by the certbot shipped with debian jessie. My understanding is that my server settings are stored in the /etc/letsencrypt folder.
When installing certbot, I’d like to ensure my settings are preserved so I don’t need to re-apply for a new certificate. Could one someone please confirm if my assumtions are correct?
Shall I just remove the old git clone folder, delete the existing cron task for renewal, install certbot and create a new cron task?
If you're downgrading to an older version of Certbot, there may be compatibility issues when renewing. Certbot will probably show a warning, but actual problems are rare.
Pretty much.
The Certbot package will install a cron job and maybe a systemd timer. You shouldn't have to set one up.
However, if the old cron job was running some sort of hooks (e.g. to reload a server), that may have to be configured somehow.