nix flake update does update other referenced flakes, but not nixpkgs. my flake is a longer business, here's the inputs section:

inputs = {
    nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05";
    nixpkgs-unstable.url = "github:NixOS/nixpkgs/nixos-unstable";
    utils.url = "github:numtide/flake-utils";
    home-manager = {
      url = "github:nix-community/home-manager/release-24.05";
    };
    colmena = {
      url = "github:zhaofengli/colmena/v0.3.2";
      inputs.utils.follows = "utils";
    };
    dsa41heldendokument = {
      url = "github:flyx/DSA-4.1-Heldendokument";
      inputs.nixpkgs.follows = "nixpkgs";
      inputs.utils.follows = "utils";
    };
    nimyaml = {
      url = "github:flyx/NimYAML";
      inputs.utils.follows = "utils";
    };
    nyarna-web = { url = "github:nyarnalang/website"; };
  };