nix flake update with no arguments updates every input in flake.lock to the latest revision its reference allows. On a flake with several inputs this produces a large, hard-to-review diff and can pull in an unrelated breaking change while trying to bump one dependency.
The single-input form changed. Older Nix used nix flake lock --update-input nixpkgs. Nix 2.19 and later accept input names as positional arguments to nix flake update, so nix flake update nixpkgs updates only that input, and the older flag is deprecated. Scripts written against one form fail on the other, and the error is a usage message rather than something searchable.
An input pinned by follows, such as making a dependency's nixpkgs point at the top-level one, is not updated independently and does not appear as a separate lock entry. Deduplicating inputs with follows is worth doing precisely because it shrinks the lock file and prevents two versions of nixpkgs being evaluated, which roughly doubles evaluation time and store usage.