I'm afraid it looks like your VPS has already been taken over. It's basically impossible to get rid of malware once a system has been compromised. You have no chance of really knowing what the attackers did, what has been manipulated or changed, where a backdoor (or ten backdoors) might be, and so on and so forth.
Judging from the fact that you can't "see" files and directory that are actually there, the attackers have probably compromised the VPS all the way and can do anything they'd like. They basically took away from you any tools to do anything against it.
There's only one way: Get rid of the VPS and make sure the provider deletes it properly. It can't be salvaged any more. Then, start over with a new VPS and better security this time. To name just a few aspects, use better passwords or strong key-based authorization, always be diligent with updates, don't use software from dubious sources, don't give anybody access you don't completely trust and so on and so forth.
Don't transfer any file, any database records or basically anything from the old VPS to the new. For all you know, anything might be compromised and just give the attacker the keys to the new VPS the minute it's set up. Remember, the attackers already own the old VPS to the degree that they can control what you do or don't "see".
If you've got backups that you know(!) are from before the intrusion (and that haven't been stored on the old VPS, obviously), you might think about using them for the new VPS. But that's still a risk, because it's hard to say when the initial intrusion really occured.
I'm sorry I can't give you a more positive outlook, but that's basically the only chance you've got. Remember, the internet is international. The moment a system can be reached from the internet, attackers from all over the world, from pole to pole, will try to compromise it and use for themselves, often by using automated attack tools. You can't be too paranoid when security is concerned.
.X17-unix
files. – Pilot6 Nov 15 '19 at 10:33