I see on various posts that people are using some sort of automatic nginx configuration. For example a user mentions it here: Seafile In Docker - Trigger Nginx Config Regeneration.
I didn’t find anywhere in the instructions to do this, only the manual install: HTTPS with Nginx - Seafile Admin Manual
How does one have nginx automatically configured?
They use docker deployment.
The seafile container provides its own nginx server, which is automatically configured with the environment variables declared in the compose file.
Thank you, that’s very helpful 
Any idea if re-installing seafile ontop of an existing seafile is possible? I was thinking of keeping seafile-data and the mysql folder but nuking the confs and the rest to start over.
Yes it is, but it’s not what I would recommend, unless you have plenty of data and/or users.
Wiping everything and then reupload all data is more friendly.