Bitnami bncert-tool failing on trying to enable auto renewal of ssl certificate

On my lightsail instance I have tried to use the bncert-tool to setup an SSL cert, but it fails on the final part which is enabling auto-renewal. I got it working by manually renewing it https://aws.amazon.com/premiumsupport/knowledge-center/lightsail-bitnami-renew-ssl-certificate/ (It kept renewing successfully but would not show on the website, except for the first time, which I have no idea why?

2023/03/16 22:59:39 [INFO] [MYDOMAIN] acme: Trying renewal with 2158 hours remaining
2023/03/16 22:59:39 [INFO] [MYDOMAIN] acme: Obtaining bundled SAN certificate
2023/03/16 22:59:39 [INFO] [MYDOMAIN] AuthURL: https://acme-v02.api.letsencrypt.org
/acme/authz-v3/
2023/03/16 22:59:39 [INFO] [MYDOMAIN] acme: authorization already valid; skipping c
hallenge
2023/03/16 22:59:39 [INFO] [MYDOMAIN] acme: Validations succeeded; requesting certi
ficates
2023/03/16 22:59:40 [INFO] [MYDOMAIN] Server responded with a certificate.

And now I've reached the limit of 5 certs) but then I tried to use bncert again and now no method is working. But regardless I would like to get the automatic method working if possible.

Domain MYDOMAIN did not pass HTTP challenge validation

https://docs.bitnami.com/google/how-to/understand-bncert/#certificates-not-renewed-automatically This page lists a solution but I still can't manage to get it working. I'm not sure if I have set the flags in the correct place?

  RewriteCond %{REQUEST_URI} !^/\.well-known

  ProxyPass /.well-known !

I placed them in my virtual host files myapp-https-vhost.conf

  <VirtualHost _default_:443>
  RewriteCond %{REQUEST_URI} !^/\.well-known

    ServerAlias *

    SSLEngine on

    SSLCertificateFile "/opt/bitnami/apache/conf/MYDOMAIN.crt"

    SSLCertificateKeyFile "/opt/bitnami/apache/conf/MYDOMAIN.key"

    DocumentRoot "/home/bitnami/htdocs/staging-api"

    <Directory "/home/bitnami/htdocs/staging-api">

      Require all granted

    </Directory>

    ProxyPass /.well-known !

    ProxyPass / http://localhost:3000/

    ProxyPassReverse / http://localhost:3000/

  </VirtualHost>

myapp-http-vhost.conf

  <VirtualHost _default_:80>
  RewriteCond %{REQUEST_URI} !^/\.well-known

    ServerAlias *

    DocumentRoot "/home/bitnami/htdocs/staging-api"

    <Directory "/home/bitnami/htdocs/staging-api">

      Require all granted

    </Directory>

    ProxyPass /.well-known !

    ProxyPass / http://localhost:3000/

    ProxyPassReverse / http://localhost:3000/

  </VirtualHost>

I also placed it in the public/.htaccess file because someone suggested it should go there.

    Options -MultiViews
    RewriteEngine On
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteRule ^ index.html [QSA,L]
    RewriteCond %{REQUEST_URI} !^/\.well-known

Not really sure where these flags are meant to go `