Everytime I get a security update then /var/run/current-system is nuked.
Is this to be expected? And it’s getting increasingly difficult to re-install… 
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I’m not sure how to interpret “/var/run/current-system is nuked”, but I suspect this just means the update is overwriting your zsh shell hook (so it isn’t getting added to PATH). This issue’s documented in macOS updates often break nix installation (updates replace path-hooks on multi-user install) · Issue #3616 · NixOS/nix · GitHub, but the TL;DR is that you can just replace the hook, using the one that should be undisturbed in /etc/bashrc as a reference.
For the reinstall problem, I’d follow the uninstall instructions and try again.
(It sounds like you have remnants of the previous install, and I’m not sure which ones. It’s also not clear if the install’s already migrated for macOS 15 Sequoia clobbers _nixbld1-4 users · Issue #10892 · NixOS/nix · GitHub. Cleaning up will be simpler at this point.)