It appears there was a deeply technical issue about the start of October in which Let’s Encrypt certificates underwent a slight change causing subtle errors in Discourse. I only found this out yesterday, but Discourse developers appear to have addressed it and I have rebuilt Discourse.
Replies from email now look like they are working properly again, although I am keeping a watchful eye on it. One user has reported an issue with replying from gmail, and I am looking into that as well.
I will keep you all posted. Pardon the dreadful pun.