Welcome Back to the Let's Encrypt Community 
My guess is that they don't like the switch from one intermediate certificate to two in fullchain.pem and chain.pem.
If you replace these two final certificates currently in both fullchain.pem and chain.pem:
https://letsencrypt.org/certs/lets-encrypt-r3.pem
https://letsencrypt.org/certs/isrg-root-x1-cross-signed.pem
with this one certificate:
https://letsencrypt.org/certs/lets-encrypt-r3-cross-signed.pem
things will likely start working again. If so, then strongSwan needs to update for the new three-certificate fullchain.