I removed all the Mongo collections that I could (graylog, config and local). I had to leave “Admin”.
After restarting the services (or rebooting the server), the collections are recreated.
I think this person was having the same issue as I am, and asked a similar question. I don’t see an answer there either. Graylog in Docker - Certificate Broken - #2 by webboty
I am open to trying to generate a new certificate, but previously those were done via the web interface GUI, and I am not sure I can replicate everything on my own via command line.