If you mean by ‘start from scratch’ uninstall everything, no, don’t do that.
Don’t try to delete anything, certificates created are outside your control and deleting them solve nothing.
However, you have to restart a new request. How it’s done depends on your client, and possibly how you used it. Since you did not share this information by avoiding to fill the default help form, it’s not possible to help your further.
I really do not know what is the point of knowing the domain, as I do not have any problem with mydomain.com but need to get www. section added to it. You just need to say for example the you can use this and that commands. The same as written in https://lengstorf.com/code/deploy-nodejs-ssl-digitalocean/ link
However, I could share the nginX if it helps to hep