You can read the not-yet-merged documentation regarding this part here:
https://github.com/YunoHost/doc/blob/742532acae8e3c9a92ff60e2ebe97889d4c632bf/certmanager.md#i-manually-installed-my-lets-encrypt-certificates
Quoting it:
I manually installed my Let’s Encrypt certificates
You should go in your nginx configuration, and remove the letsencrypt.conf (or whatever you called the file containing the location ‘/.well-known/acme-challenge’ block) for each of your domains. Remove your certificate renewer cron job in /etc/cron.weekly/, and backup and remove your /etc/letsencrypt/ folder.
Then run :
yunohost domain cert-install your.domain.tld --force
for each of your domains you want a Let’s Encrypt certificate.
You can follow the discussion regarding the release here Stable release 2.5