First thanks a lot to Jeff! I've not found how to solve but I understand what's happening.
Virtualmin wants to have the certificates located in the virtual server "home" folder. So if my virtual server name is "my_server", Virtualmin search the files in home/my_server/. And in fact at this location, I have certificates files (ssl.cert, ssl.key...) but they are old ones (from February).
But when renewal occur, Let's Encrypt put the files in his own directory, at "etc/letsencrypt/live/domaine_name/"
I don't know if the location has changed in February or if a symlink has been broken. But when I visit my Website with a browser, Apache use the keys in etc/letsencrypt/live/domaine_name/ while Virtualmin continue searching for the files in the virtual server folder, where he found old keys.
Here are some details: https://github.com/virtualmin/virtualmin-gpl/issues/20
Edit: I've made symlink like this:
ln -s /etc/letsencrypt/live/my_domaine/cert.pem ssl.cert
ln -s /etc/letsencrypt/live/my_domaine/cert.pem ssl.combined
ln -s /etc/letsencrypt/live/my_domaine/privkey.pem ssl.key
ln -s /etc/letsencrypt/live/my_domaine/chain.pem ssl.ca
ln -s /etc/letsencrypt/live/my_domaine/fullchain.pem ssl.everything
and now it seems to be OK.
perl virtualmin-get-domains-ssl-status.plat forum.virtualmin.com/t/…; does it provide anything useful? Also interesting is forum.virtualmin.com/t/…