Trying to use Let's Encrypt + Cloudflare

[cean]

Will Let’s Encrypt continue to renew automatically within 90 days?

Yes. It should do. Cerbot does that. I do not think Discourse dev team would have skipped that feature.

Edit:

Setting up HTTPS support with Let's Encrypt

Installs the cert into the right directory that nginx expects. At the same time, it adds a cron job that runs a daily cert renewal check . This will automatically renew your cert. Nothing happens if cert has not expired. If the certificate does expire, you’ll get an email about it from Let’s Encrypt at the email address you provided during setup.