I think it's fixed now. For some reason I had to make a minor change to the web server configuration that was seemingly unrelated to the SSL renewal, and then it renewed fine. I might be doing some more server maintenance over the next few days, so let me know if anything is not working as expected. I am also tempted to do a distribution upgrade from Ubuntu 16 to 18, but I'm not quite brave enough yet. I may test that on another server first.
By the way, we had a 9lb 2oz boy and we had to evict him a week after his due date. Beside that, everything is looking good. It's been quite a week so far.