Cloning the VM is indeed a convenient way of duplicating a Moodle site, albeit an overkill. Of course there is a whole series of adjustments you need to do in and for the new Moodle. Pointing the new IP address to the new (sub)domain, configuring the web server to react properly to requests addressed to that domain, editing config.php of the new instance, running /replace/ script after all that,..
If "we have sent clone request to VPS provider and they did this, I've no detail information about what exactly they did" is the case, I assume the provider knows Moodle. And also careful enough to avoid common pitfalls, like the new Moodle not hitting the original database, in case the DB server is external to the VM!
If "we have sent clone request to VPS provider and they did this, I've no detail information about what exactly they did" is the case, I assume the provider knows Moodle. And also careful enough to avoid common pitfalls, like the new Moodle not hitting the original database, in case the DB server is external to the VM!
P.S. If you are looking for a multi-tenant Moodle, keep it a separate topic. This one is about the errors you are getting right now.