Thank you, replacing agda with haskellPackages.agda did work.
with import <nixpkgs> { };
let
my-agda = agdaPackages.override {
Agda = haskellPackages.Agda.overrideAttrs {
patches = [ (fetchpatch { ... }) ];
};
}.agda.withPackages (p: [ p.standard-library ]);
in
mkShell {
buildInputs = [ my-agda ];
}
Strange though. Could a nix package rebuild even if its source was unchanged? I remember well that I never attempted this solution before, and I remember just as well agda building from source.