I received the email saying my self-hosted Ubuntu server used TLS-SNI-01 on 2018-11-28. I followed the link to the instructions on this site, but could not find anything wrong with my server. Certbot version is 0.28.0. There is no mention of tls-sni-01 in my config files. The results of certbot renew --dry-run indicate all renewals succeeded using http-01 challenge.
Neither the email nor the pinned topic here reflect this situation. It appears the email was generated in error, or the Ubuntu PPA (updated 2018-12-14) has already solved this problem.
The system can’t detect what version you are using - when compared to what version you did use last to get a cert.
Any new use would (if successful) get a new cert - which would not remove then fact that the previous cert was obtained with an older version and will soon be expiring.
Even if they contain the same name(s) and are from the same IP and from the same account - there is no way to know they cam from the same system, nor if the newer version replaced the older version.
[What if you installed to second client on the same system? One could be new and old could be old.]
So, you see, there is no real way to know (from outside your own system) which version of which client is currently in use.
Yes it can detect this by waiting for the 3-month certificate expiry period after the software update has been pushed. There could still be corner cases, but I imagine it would have been much smoother than blasting out emails a month after the patch.