After using the bncert-tool on my Wordpress Mutisite all sites are down

When the bncert-tool runs on a Lightsail WordPress instance, it can sometimes overwrite configuration files, which appears to be what happened in your case. Unfortunately, there isn't a built-in "undo" feature for the bncert-tool, but you can take several steps to restore functionality:

1. Check for backups: First, see if there are any automatic backups of your configuration files. Sometimes the tool creates .bak files when it makes changes.

2. Restore from a Lightsail snapshot: If you have a recent snapshot of your Lightsail instance from before running the bncert-tool, you could restore from that snapshot.

3. Manually fix the configurations:

• For nginx: Restore the proper multisite configuration in your nginx config files
• For PHP-FPM: Check the php-fpm configuration files (typically in /opt/bitnami/php/etc/php-fpm.d/) and ensure they have the correct settings

4. Reset certificates: You might need to reset the certificates using the Bitnami documentation approach. This involves backing up current certificates and then reinstalling them.

5. Restart services: After fixing configurations, restart the services:

sudo /opt/bitnami/ctlscript.sh restart

6. Check logs: Review error logs to identify specific issues:

• Nginx logs: /opt/bitnami/nginx/logs/
• PHP-FPM logs: /opt/bitnami/php/logs/

For the PHP-FPM issues specifically, check that the socket path in your nginx configuration matches the one in your php-fpm configuration, and that the user permissions are correct.

If these steps don't resolve the issue, you might need to consider restoring from a backup or snapshot if available, or contacting AWS support for more specialized assistance with your multisite configuration.
Sources
Replacing a TSL certificate on LightSail | AWS re:Post
Lightsail/WordPress Site and Subdomain Suddenly Down – Unable to Access | AWS re:Post
WordPress site on Lightsail can't connect to any HTTPS resource | AWS re:Post