How to get around bad package updates?

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Sorry, I just noticed you are using flakes. Instead of using fetchTarball you can more easily use a flake input.

inputs.nixpkgs-2.url = "github:NixOS/nixpkgs/deadbeef";

(replace the commit hash, of course.)

Then, you can use something akin to (assuming you’ve passed your inputs into the module system):

{ inputs, pkgs, config, ... }:
let
  pkgs2 = import inputs.nixkpgs-2 {
    inherit (pkgs.stdenv.hostPlatform) system;
    inherit (config.nixpkgs) config;
  };
in
{
  # config settings ...
}

and use pkgs2.mkvtoolnix as needed, within that config block

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