I can only comment on the process with the hosted builder. If you follow Erel's video (
Creating a certificate and provisioning profile) everything will work. The csr file is created as soon as you create a private sign key. Typical advice is to delete all files in the keys folder and start from scratch.
If you've still got a working csr file, you can use it to create the distribution certificate and the provisioning profile on the apple developer website. As far as I know you don't need a new csr file for that (at least it worked for me when I had to renew my certificates).