Your custom domain is fully set up on its own: its DNS record has propagated, ownership is verified, and its SSL certificate is valid. Its DNS points to a dedicated target that belongs to the custom domain entry itself, not to either of the generated domains, so it keeps working whether or not the generated domains exist.

All three domains are attached to the same service in the same environment, so the generated domains are only extra public addresses for that service. Removing them does not touch your deployment, your hosting, or the custom domain's certificate. The only effect is that anything still pointing at those addresses (bookmarks, webhooks, or settings that reference them) will stop reaching the site.

We can't tell from our side which of the two generated domains the dashboard labels as primary, but the answer doesn't change the procedure, because neither one carries traffic for your custom domain. The safest order is to confirm your custom domain loads over https, delete one generated domain, check the site again, then delete the other. If you ever want one back, you can generate a new one from the same Public Networking section, though it may get a different address.