Cannot access VestaCP and website shows The Apache2 Default Page

[TheComputerDude]

Hello I was trying to get iRedMail to work since Vesta's default mail server did not work correctly (Installed with SOGo) and now it seems that the apache2 conf settings reset, I kept a backup of the old Apache2 settings from VESTA and I entered those in and still the default page is still there it also seemed to have deleted the sites-available because it only shows 000-default.conf default default-ssl default-ssl.conf is this normal? Also, I did restart NGINX and Apache2 manually and still that "It works" page is there any way of fixing this?
The domains I own are:
allmotti.com
allmotti.xyz
socialscribe.xyz
viduro.xyz
pictasia.me
and others.
(I host my site at home.)
EDIT: I am using Ubuntu 16.04
I stopped the apache2 process and the website still shows the apache default page and when I stop nginx it says refused to connect of course so it might be nginx because I modified the nginx config lately.

[ScIT]

This sounds like a complicated problem, do you not think it would be easier to reinstall the server then migrate the domains? Maybe you can work with v-backup-user / v-restore-user over cli, maybe the commands are still working.

[TheComputerDude]

That's what I ended up doing.