diff --git a/tests/functional/flakes/flakes.sh b/tests/functional/flakes/flakes.sh
index ea58d3b41..f5adb8d33 100644
--- a/tests/functional/flakes/flakes.sh
+++ b/tests/functional/flakes/flakes.sh
@@ -77,10 +77,6 @@ git -C $flake1Dir add $flake1Dir/foo
 echo -n '# foo' >> $flake1Dir/flake.nix
 git -C $flake1Dir commit -a -m 'Foo'
 
-# Check that store symlinks inside a flake are not interpreted as flakes.
-nix build -o $flake1Dir/result git+file://$flake1Dir
-nix path-info $flake1Dir/result
-
 # set up lockfiles for later tests
 nix build -o $TEST_ROOT/result $flake2Dir#bar --commit-lock-file
 nix build -o $TEST_ROOT/result $flake3Dir#xyzzy
@@ -170,13 +166,3 @@ nix build -o $TEST_ROOT/result flake3#sth
 mv $flake2Dir.tmp $flake2Dir
 mv $nonFlakeDir.tmp $nonFlakeDir
 nix build -o $TEST_ROOT/result flake3#xyzzy flake3#fnord
-
-# Test doing multiple `lookupFlake`s
-nix build -o $TEST_ROOT/result flake4#xyzzy
-
-# Test 'nix flake update' and --override-flake.
-nix flake lock $flake3Dir
-[[ -z $(git -C $flake3Dir diff master || echo failed) ]]
-
-nix flake update --flake "$flake3Dir" --override-flake flake2 nixpkgs
-[[ ! -z $(git -C "$flake3Dir" diff master || echo failed) ]]
diff --git a/tests/functional2/flakes/test_cli.py b/tests/functional2/flakes/test_cli.py
index 9ef03e0ac..abff4725d 100644
--- a/tests/functional2/flakes/test_cli.py
+++ b/tests/functional2/flakes/test_cli.py
@@ -500,6 +500,25 @@ class TestBuild:
             # check that the lockfile was changed
             assert git(flake3, "diff", "HEAD").stdout_s
 
+    def test_deep_build(self, nix: Nix, flake3: Path):
+        """test builds that need recursive flakeref resolution"""
+        # flake4 points to flake3 which thus needs locked
+        nix.nix(["flake", "lock", flake3]).run().ok()
+        nix.nix(["build", "flake4#xyzzy"]).run().ok()
+
+
+@pytest.mark.usefixtures("registry")
+def test_update_with_override_flake(nix: Nix, flake3: Path, git: Git):
+    nix.nix(
+        ["flake", "update", "--flake", flake3, "--override-input", "flake2", "nixpkgs"]
+    ).run().ok()
+    assert git(flake3, "diff", "HEAD").stdout_s
+
+
+def test_symlinks_in_flakes_are_not_flakes(nix: Nix, flake1: Path):
+    nix.nix(["build", "-o", flake1 / "result", f"git+file://{flake1}"]).run().ok()
+    nix.nix(["path-info", flake1 / "result"]).run().ok()
+
 
 @pytest.mark.usefixtures("registry")
 def test_flakes_gcroots(nix: Nix, flake1: Path, flake2: Path):