hlissner even suggests a workaround:

# Update MELPA
cd ~/.emacs.d/.local/straight/repos/melpa
git pull

# Clear straight's cache
rm -f ~/.emacs.d/.local/straight/build-cache.el
doom sync

But since I've set up doom through nixos (presumably), ~/.emacs.d/ is empty.

In reply to @asbjorn:olli.ng
TL;DR
does anyone know how to update the MELPA repository indexes manually on NixOS?

You can add a package manually if it is missing, for instance I have:

      programs.doom-emacs = {
        enable = true;
        doomPrivateDir = ./doom.d;
        emacsPackagesOverlay = final: prev: {
          ob-ammonite = with final;
            (trivialBuild {
              src = pkgs.fetchFromGitHub {
                owner = "zwild";
                repo = "ob-ammonite";
                rev = "39937dff395e70aff76a4224fa49cf2ec6c57cca";
                sha256 = pkgs.lib.fakeSha256;
              };
              pname = "ob-ammonite";
              packageRequires = [ s dash editorconfig ];
            });
        };
      };