I use home-manager as my profile management layer so I might not understand your setup fully, but Flakes dont really mesh with channels. They instead use a flak

I use home-manager as my profile management layer so I might not understand your setup fully, but Flakes dont really mesh with channels. They instead use a flake.lock and so you would need to do a `nix flake update` to get the flake-managed packages updated. EDIT: you also might be able to inject your local channels "pkgs" definition into the flake so that they reference the same versions. e.g. for home-manager with flakes you would do it like this inputs = { nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable"; home-manager = { inputs.nixpkgs.follows = "nixpkgs"; # <- deduped version of packages url = "github:nix-community/home-manager"; }; };