I can’t find the thread where I first saw this. Someone had problems saving pages served with certificates from Let’s Encrypt in the Internet Way Back Machine (Internet Archive).
I sent them an email and I got a reply today saying they’d update their certificate store and that any website using Let’s Encrypt certificates should be working now. I tried saving the Hello World page, and sure enough it was now successfully saved to the archives.
Using Let’s Encrypt no longer means your website can’t be saved for prosperity.