It’s unlikely to be a Cloudflare proxy issue. It’s an issue with the origin. Have you disabled the proxy to verify SSL is still working properly on the domain after the upgrade?
Thank you for your response, but I don’t understand what “an issue with the origin” means exactly.
To try to troubleshoot this issue, I created two new subdomains on the same server in the OP.
https://test1.hush.is/ is using a Let’s Encrypt SSL cert without Cloudflare Proxy. This is working perfectly fine.
https://test11.hush.is/ is using a Let’s Encrypt SSL cert & was working perfectly fine until Cloudflare Proxy was turned onto it. This domain is having the same issue as I reported in the OP.
Any suggestions on how to better troubleshoot this?