Nix flake update, path '/nix/store/*-source/flake.nix` does not exist

Help
1

I’m trying to run nix flake update but get this error

error:
       … while updating the lock file of flake 'git+file:///home/river/dev/github.com/iainvm/nix?ref=refs/heads/main&rev=bd2027c1896c29083b442eff32c7a793bddc98bd'

       … while updating the flake input 'flake-utils'

       error: path '/nix/store/01x5k4nlxcpyd85nnr0b9gm89rm8ff4x-source/flake.nix' does not exist

There are no changes to the my configuration so no files to add to git

Even reducing the flake down to this for testing gives the same error

{
  description = "My Nix configs";

  inputs = {
    nixpkgs = {
      url = "github:NixOS/nixpkgs/nixos-unstable";
    };

    flake-utils = {
      url = "github:numtide/flake-utils";
    };
  };

  outputs = {
    self,
    nixpkgs,
    flake-utils,
    ...
  } @ inputs:
    flake-utils.lib.eachDefaultSystem (system: {
      devShells = import ./devShells/configuration.nix {
        inherit inputs system;
      };
    });
}

I’m unsure how to even debug this to tell why it can’t find a flake the system seems to be dependent on

2

It appears that the file is missing, try running nix-store --verify --check-contents --repair

3

That seems to have fixed it. Thank you!
Any ideas on how I could have got into this state?