Am I posting sites correctly?

Question

Search Engine Optimization

Good.
Comrades, please comment on the situation:
There is an "important site". Works on http and https. Located on a virtual machine in an nginx environment ...
I, being a crooked "admin", did not pay attention to the fact that the https host configured for "important site" turns out to be the default host for all other sites on this server. These sites opened over https with content from "important site". Well, of course... the default host. The result of negligence: Yandex redefined the main mirror for "important site" to one of the available on the server. Of course, according to the search phrase, instead of “important site”, the first place was “other site”.
What measures were taken: a real http and https hosts were created by default, which give a 404 response. A direct campaign was launched on Yandex, so that at least for some requests it would give out an “important site” before the search results. Yandex said to wait for the update of the issuance - 2-3 weeks.
Can you tell me if I've taken the right steps? Would you do something else?
Some recommend moving the “important site” to a separate virtual machine, so that on the virtual machine where the “important site” is now located, https does not respond at all. I think this is superfluous, because for https for other sites, and so 404 and Yandex sees it. And is it the fault of the site developers that they did not indicate the main mirror in robots.txt during development?

Answer 1

The one who should have indicated in robots.txt, but did not, is to blame.
Who should have been - either the one in whose duties it is prescribed (who is responsible for the search engine optimization of the site), or the one in whose interests it is (the owner of the site).
You explain how you overcame the merging of domains through some kind of fraud with virtual machines, which is not entirely clear how it is connected at all.
Do so. as it should be - so that each domain gives only its own site both via http and http, while specifying the main mirror in the robots for each of the domains.

Answer 2

I think we still need to transfer to another server to show the appearance of useful work =)