Accidentally the files in /etc/letsencrypt/domain.com where deleted. Also the files in crs folder. I managed to restore them from my daily backup,but now when I hit Https://domain.com, I get cert error. In fact it is using the cert from another domain that is also hosted on the same server!! How can I tell ispconfig to use the right cert?
Do you get the wrong ssl cert but the right website is shown after accepting the error or do you the wrong website (you enter a.com in the browser and get ssl cert and content of b.com)? If you get the ssl cert and content of b.com, then a.com has no ssl enabled. check a.com again if SSL and let's encrypt checkboxes stay ticked 1-2 minutes after you activated them.
Letsencrypt checkboxes stay ticket!. The right website is shown when I accept the error. Letsencrypt log shows that too many requests for certificate for the same domain has been made, so only after 7 days the will issue a new one. But I have the files after the backup, meaning I have the cert. How can I tell ispconfig to use it????
Untick the sll and le checkbox, save, enable it again. Before you do that, ensure to update to ispconfig git-stable branch with ispconfig_update.sh command.
You cannot issue new certs for now, so try to check the links in your website ssl folder then. To which LE folder its certs redirect to. It could already has multiple folders, so you'll need to fix their links.
ISPConfig will reuse existing SSL certs automatically when it contains the right domain names, there should be no need to alter any symlinks on the shell then, see post #5 for the procedure.