Are you sure? I mean, “should not” or “will not”? In my case after probably the 4th discourse-setup within the same existing installation the server finally started to “time-out” (for a few days). There are many posts here advising to use ./discourse-setup when you need to modify setup details, emails etc.
There are those 3 lines in the app.yml:
## Uncomment these two lines if you wish to add Lets Encrypt (https)
- "templates/web.ssl.template.yml"
- "templates/web.letsencrypt.ssl.template.yml"
but I’m not sure whether commenting them out means the existing cert will be left/reused or there will be no cert at all.