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Without seeing the exact setup (and bearing in mind I’m no expert) - do you need multiple location (or server) blocks in nginx to point the different domains at different paths, ssl certs etc? Just thinking out loud here in the hope it triggers a spark in your mind :-)
i.e. see - https://www.digitalocean.com/community/tutorials/how-to-set-up-nginx-server-blocks-virtual-hosts-on-ubuntu-14-04-lts - this don’t take into account any ServerPilot specific config though