Yes. The three domain names are all on a single certificate, because you requested them in a single command. You can use certbot-auto certificates to see what certificates you have and what domains they cover.
It looks green from here (or at least, it did when I tried it a moment ago, but now it seems to be down entirely).
Maybe a browser extension is interfering?
That warning doesn't appear to be fatal. However, if you're using nginx you can select the nginx plugin instead of apache by adding the --nginx option to the certbot command.
Whoops, sorry, jmorahan, I stopped nginx there while worked on tweaking default nginx file. It is up now and running.
Thank you!!! I went to check on another computer, and both are indeed green secured https. On my laptop, though, one is still grey, and the “Secure” word is missing. But, a huge load off.
Appreciate the cert-checking command. Yay!
The red warning was because nginx was still running. After stopping, generating a certificate for another bunch of domains went smoothly.
One last question: I am not quite clear, if certificate regeneration (running the command again) can be performed at any time? Without any changes in config files (either under letsencrypt, or in nginx)? Or, letsencrypt will sense that a certificate already exists, and won’t create a new one?
Greyed logos without “Secure” can be a problem of insecure elements on the page, like images or scripts pulled in through http:// instead of https://.
If you notice the green logo and secure is gone, you should open the developer toolbar of your browser and go to the Console, reload the page and check what notice/warning you get. It should warn you about insecure elements.