Handling all cases of pre-existing Nix installations, (multi-user, single-user, incomplete, broken, etc) is something we are trying to improve. There is also upstream community work going into improving this experience and we will adopt that as it becomes available. The .deb installs Nix for you, so your best bet is to remove the existing installation (https://nixos.org/manual/nix/stable/installation/installing-...) and try the native installer.

Regardless, I'd like to fix the scenario you are in. Would you be willing to send in some logs or details?