Can I use multiple repositories with a single kopia inscance?
When I create another repository all my existing files in /root/.config/kopia/ are overwritten…
Nobody can see your screen and what you are doing. Without more details it is just another story I doubt anybody can help with.
You could have given an answer to my question… 
To be more precise, can I specify more than one repo in the config file and use multiple repos simultaneously running one kopia instance?
one config file one repo but you can have multiple config files. Check docs for --config-file flag.
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Thanks. Found it in the docs a few seconds ago.
What would in your opinion be the best way to backup multiple servers to the same physical backup disk?
Multiple repositories and kopia server instances where all my machines connect to?
Or is it even possible that one kopia server instance deals with multiple repositories at the same time?
IMO it would be one repository behind kopia server. This way you benefit the most from deduplication and keep things simple. This is exactly what server is for…:
By default, every user of Kopia repository directly connects to an underlying storage using read-write access. If the users who share the repository do not entirely trust each other, some malicious actors can delete repository data structures, causing data loss for others.
Repository Server allows an instance of Kopia to proxy access to the underlying storage and has Kopia clients proxy all access through it, only requiring a username and password to talk to the server without any knowledge of repository storage credentials.
In repository server mode, each user is limited to seeing their own snapshots and policy manifest without being able to access those from another user account.
So the idea here could be to control snapshot visibility by using different users for different machines, right?
A user for a remote server would most likely have only APPEND permissions but nothing more. Sounds feasible.
That’s exactly how we do it. Beware though, that the “master” user has access to all data.