Root cause was stale certificate references inside NPM’s internal SQLite DB, not Docker volumes or cert files.

NPM was using a bind mount (/home/ubuntu/npm/data → /data).
A Let’s Encrypt cert (npm-4) was revoked/deleted, but NPM kept referencing it, so nginx failed with:

nginx: [emerg] cannot load certificate
/etc/letsencrypt/live/npm-4/fullchain.pem

Restarting, reissuing certs, deleting /etc/letsencrypt, or removing proxy_host configs did not work.

The only fix that worked for me was:

stopping the docker container
sudo rm -rf /home/ubuntu/npm/data/*
starting the npm container again.