diff --git a/pkgs/clan-cli/clan_cli/vars/_types.py b/pkgs/clan-cli/clan_cli/vars/_types.py
index 670bf2b5c..ea4d20999 100644
--- a/pkgs/clan-cli/clan_cli/vars/_types.py
+++ b/pkgs/clan-cli/clan_cli/vars/_types.py
@@ -1,9 +1,9 @@
 import logging
-import shutil
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from pathlib import Path
 
+from clan_cli.errors import ClanError
 from clan_cli.machines import machines
 
 log = logging.getLogger(__name__)
@@ -113,6 +113,13 @@ class StoreBase(ABC):
     def is_secret_store(self) -> bool:
         pass
 
+    def backend_collision_error(self, folder: Path) -> None:
+        msg = (
+            f"Var folder {folder} exists but doesn't look like a {self.store_name} secret."
+            "Potentially a leftover from another backend. Please delete it manually."
+        )
+        raise ClanError(msg)
+
     def rel_dir(self, generator_name: str, var_name: str, shared: bool = False) -> Path:
         if shared:
             return Path(f"shared/{generator_name}/{var_name}")
@@ -145,12 +152,6 @@ class StoreBase(ABC):
         else:
             old_val = None
             old_val_str = "<not set>"
-        directory = self.directory(generator_name, var_name, shared)
-        # delete directory
-        if directory.exists():
-            shutil.rmtree(directory)
-        # re-create directory
-        directory.mkdir(parents=True, exist_ok=True)
         new_file = self._set(generator_name, var_name, value, shared, deployed)
         if self.is_secret_store:
             print(f"Updated secret var {generator_name}/{var_name}\n")
diff --git a/pkgs/clan-cli/clan_cli/vars/public_modules/in_repo.py b/pkgs/clan-cli/clan_cli/vars/public_modules/in_repo.py
index 697fdcc43..ce5c102d1 100644
--- a/pkgs/clan-cli/clan_cli/vars/public_modules/in_repo.py
+++ b/pkgs/clan-cli/clan_cli/vars/public_modules/in_repo.py
@@ -1,3 +1,4 @@
+import shutil
 from pathlib import Path
 
 from clan_cli.errors import ClanError
@@ -23,14 +24,22 @@ class FactStore(FactStoreBase):
         shared: bool = False,
         deployed: bool = True,
     ) -> Path | None:
-        if self.machine.flake.is_local():
-            file_path = self.directory(generator_name, name, shared) / "value"
-            file_path.parent.mkdir(parents=True, exist_ok=True)
-            file_path.touch()
-            file_path.write_bytes(value)
-            return file_path
-        msg = f"in_flake fact storage is only supported for local flakes: {self.machine.flake}"
-        raise ClanError(msg)
+        if not self.machine.flake.is_local():
+            msg = f"in_flake fact storage is only supported for local flakes: {self.machine.flake}"
+            raise ClanError(msg)
+        folder = self.directory(generator_name, name, shared)
+        if folder.exists():
+            if not (folder / "value").exists():
+                # another backend has used that folder before -> error out
+                self.backend_collision_error(folder)
+            shutil.rmtree(folder)
+        # re-create directory
+        file_path = folder / "value"
+        folder.mkdir(parents=True, exist_ok=True)
+        file_path.parent.mkdir(parents=True, exist_ok=True)
+        file_path.touch()
+        file_path.write_bytes(value)
+        return file_path
 
     # get a single fact
     def get(self, generator_name: str, name: str, shared: bool = False) -> bytes:
diff --git a/pkgs/clan-cli/clan_cli/vars/secret_modules/sops.py b/pkgs/clan-cli/clan_cli/vars/secret_modules/sops.py
index 228a10a35..cd2593bd2 100644
--- a/pkgs/clan-cli/clan_cli/vars/secret_modules/sops.py
+++ b/pkgs/clan-cli/clan_cli/vars/secret_modules/sops.py
@@ -1,7 +1,8 @@
+import json
 from pathlib import Path
 
 from clan_cli.machines.machines import Machine
-from clan_cli.secrets.folders import sops_secrets_folder
+from clan_cli.secrets.folders import sops_machines_folder, sops_secrets_folder
 from clan_cli.secrets.machines import add_machine, add_secret, has_machine
 from clan_cli.secrets.secrets import decrypt_secret, encrypt_secret, has_secret
 from clan_cli.secrets.sops import generate_private_key
@@ -40,6 +41,18 @@ class SecretStore(SecretStoreBase):
     def store_name(self) -> str:
         return "sops"
 
+    def machine_has_access(
+        self, generator_name: str, secret_name: str, shared: bool
+    ) -> bool:
+        secret_path = self.secret_path(generator_name, secret_name, shared)
+        secret = json.loads((secret_path / "secret").read_text())
+        recipients = [r["recipient"] for r in secret["sops"]["age"]]
+        machines_folder_path = sops_machines_folder(self.machine.flake_dir)
+        machine_pubkey = json.loads(
+            (machines_folder_path / self.machine.name / "key.json").read_text()
+        )["publickey"]
+        return machine_pubkey in recipients
+
     def secret_path(
         self, generator_name: str, secret_name: str, shared: bool = False
     ) -> Path:
@@ -53,16 +66,28 @@ class SecretStore(SecretStoreBase):
         shared: bool = False,
         deployed: bool = True,
     ) -> Path | None:
-        path = self.secret_path(generator_name, name, shared)
-        encrypt_secret(
-            self.machine.flake_dir,
-            path,
-            value,
-            add_machines=[self.machine.name],
-            add_groups=self.machine.deployment["sops"]["defaultGroups"],
-            git_commit=False,
-        )
-        return path
+        secret_folder = self.secret_path(generator_name, name, shared)
+        # delete directory
+        if secret_folder.exists() and not (secret_folder / "secret").exists():
+            # another backend has used that folder before -> error out
+            self.backend_collision_error(secret_folder)
+        # create directory if it doesn't exist
+        secret_folder.mkdir(parents=True, exist_ok=True)
+        if shared and self.exists_shared(generator_name, name):
+            # secret exists, but this machine doesn't have access -> add machine
+            # add_secret will be a no-op if the machine is already added
+            add_secret(self.machine.flake_dir, self.machine.name, secret_folder)
+        else:
+            # initialize the secret
+            encrypt_secret(
+                self.machine.flake_dir,
+                secret_folder,
+                value,
+                add_machines=[self.machine.name] if deployed else [],
+                add_groups=self.machine.deployment["sops"]["defaultGroups"],
+                git_commit=False,
+            )
+        return secret_folder
 
     def get(self, generator_name: str, name: str, shared: bool = False) -> bytes:
         return decrypt_secret(
@@ -80,10 +105,14 @@ class SecretStore(SecretStoreBase):
         )
         (output_dir / "key.txt").write_text(key)
 
+    def exists_shared(self, generator_name: str, name: str) -> bool:
+        secret_folder = self.secret_path(generator_name, name, shared=True)
+        return (secret_folder / "secret").exists()
+
     def exists(self, generator_name: str, name: str, shared: bool = False) -> bool:
         secret_folder = self.secret_path(generator_name, name, shared)
         if not (secret_folder / "secret").exists():
             return False
-        # add_secret will be a no-op if the machine is already added
-        add_secret(self.machine.flake_dir, self.machine.name, secret_folder)
-        return True
+        if not shared:
+            return True
+        return self.machine_has_access(generator_name, name, shared)
diff --git a/pkgs/clan-cli/tests/fixtures_flakes.py b/pkgs/clan-cli/tests/fixtures_flakes.py
index bc2b2cb9f..91bde35ff 100644
--- a/pkgs/clan-cli/tests/fixtures_flakes.py
+++ b/pkgs/clan-cli/tests/fixtures_flakes.py
@@ -54,6 +54,16 @@ class FlakeForTest(NamedTuple):
 from age_keys import KEYS, KeyPair
 
 
+def set_machine_settings(
+    flake: Path,
+    machine_name: str,
+    machine_settings: dict,
+) -> None:
+    settings_path = flake / "machines" / machine_name / "settings.json"
+    settings_path.parent.mkdir(parents=True, exist_ok=True)
+    settings_path.write_text(json.dumps(machine_settings, indent=2))
+
+
 def generate_flake(
     temporary_home: Path,
     flake_template: Path,
@@ -117,9 +127,7 @@ def generate_flake(
 
     # generate machines from machineConfigs
     for machine_name, machine_config in machine_configs.items():
-        settings_path = flake / "machines" / machine_name / "settings.json"
-        settings_path.parent.mkdir(parents=True, exist_ok=True)
-        settings_path.write_text(json.dumps(machine_config, indent=2))
+        set_machine_settings(flake, machine_name, machine_config)
 
     if "/tmp" not in str(os.environ.get("HOME")):
         log.warning(
diff --git a/pkgs/clan-cli/tests/test_vars.py b/pkgs/clan-cli/tests/test_vars.py
index e510c62ca..1bbec7ce6 100644
--- a/pkgs/clan-cli/tests/test_vars.py
+++ b/pkgs/clan-cli/tests/test_vars.py
@@ -8,14 +8,16 @@ from tempfile import TemporaryDirectory
 import pytest
 from age_keys import SopsSetup
 from clan_cli.clan_uri import FlakeId
+from clan_cli.errors import ClanError
 from clan_cli.machines.machines import Machine
 from clan_cli.nix import nix_eval, nix_shell, run
 from clan_cli.vars.check import check_vars
+from clan_cli.vars.generate import generate_vars_for_machine
 from clan_cli.vars.list import stringify_all_vars
 from clan_cli.vars.public_modules import in_repo
 from clan_cli.vars.secret_modules import password_store, sops
 from clan_cli.vars.set import set_var
-from fixtures_flakes import generate_flake
+from fixtures_flakes import generate_flake, set_machine_settings
 from helpers import cli
 from helpers.nixos_config import nested_dict
 from root import CLAN_CORE
@@ -152,6 +154,10 @@ def test_generate_secret_var_sops(
     assert sops_store.get("my_generator", "my_secret").decode() == "hello\n"
     vars_text = stringify_all_vars(machine)
     assert "my_generator/my_secret" in vars_text
+    # test regeneration works
+    cli.run(
+        ["vars", "generate", "--flake", str(flake.path), "my_machine", "--regenerate"]
+    )
 
 
 @pytest.mark.impure
@@ -186,6 +192,50 @@ def test_generate_secret_var_sops_with_default_group(
     assert sops_store.get("my_generator", "my_secret").decode() == "hello\n"
 
 
+@pytest.mark.impure
+def test_generated_shared_secret_sops(
+    monkeypatch: pytest.MonkeyPatch,
+    temporary_home: Path,
+    sops_setup: SopsSetup,
+) -> None:
+    m1_config = nested_dict()
+    shared_generator = m1_config["clan"]["core"]["vars"]["generators"][
+        "my_shared_generator"
+    ]
+    shared_generator["share"] = True
+    shared_generator["files"]["my_shared_secret"]["secret"] = True
+    shared_generator["script"] = "echo hello > $out/my_shared_secret"
+    m2_config = nested_dict()
+    m2_config["clan"]["core"]["vars"]["generators"]["my_shared_generator"] = (
+        shared_generator.copy()
+    )
+    flake = generate_flake(
+        temporary_home,
+        flake_template=CLAN_CORE / "templates" / "minimal",
+        machine_configs={"machine1": m1_config, "machine2": m2_config},
+        monkeypatch=monkeypatch,
+    )
+    monkeypatch.chdir(flake.path)
+    sops_setup.init()
+    machine1 = Machine(name="machine1", flake=FlakeId(str(flake.path)))
+    machine2 = Machine(name="machine2", flake=FlakeId(str(flake.path)))
+    cli.run(["vars", "generate", "--flake", str(flake.path), "machine1"])
+    assert check_vars(machine1)
+    cli.run(["vars", "generate", "--flake", str(flake.path), "machine2"])
+    assert check_vars(machine2)
+    assert check_vars(machine2)
+    m1_sops_store = sops.SecretStore(machine1)
+    m2_sops_store = sops.SecretStore(machine2)
+    assert m1_sops_store.exists("my_shared_generator", "my_shared_secret", shared=True)
+    assert m2_sops_store.exists("my_shared_generator", "my_shared_secret", shared=True)
+    assert m1_sops_store.machine_has_access(
+        "my_shared_generator", "my_shared_secret", shared=True
+    )
+    assert m2_sops_store.machine_has_access(
+        "my_shared_generator", "my_shared_secret", shared=True
+    )
+
+
 @pytest.mark.impure
 def test_generate_secret_var_password_store(
     monkeypatch: pytest.MonkeyPatch,
@@ -383,21 +433,21 @@ def test_share_flag(
 ) -> None:
     config = nested_dict()
     shared_generator = config["clan"]["core"]["vars"]["generators"]["shared_generator"]
+    shared_generator["share"] = True
     shared_generator["files"]["my_secret"]["secret"] = True
     shared_generator["files"]["my_value"]["secret"] = False
     shared_generator["script"] = (
         "echo hello > $out/my_secret && echo hello > $out/my_value"
     )
-    shared_generator["share"] = True
     unshared_generator = config["clan"]["core"]["vars"]["generators"][
         "unshared_generator"
     ]
+    unshared_generator["share"] = False
     unshared_generator["files"]["my_secret"]["secret"] = True
     unshared_generator["files"]["my_value"]["secret"] = False
     unshared_generator["script"] = (
         "echo hello > $out/my_secret && echo hello > $out/my_value"
     )
-    unshared_generator["share"] = False
     flake = generate_flake(
         temporary_home,
         flake_template=CLAN_CORE / "templates" / "minimal",
@@ -775,3 +825,47 @@ def test_migration(
     )
     assert in_repo_store.exists("my_generator", "my_value")
     assert in_repo_store.get("my_generator", "my_value").decode() == "hello"
+
+
+@pytest.mark.impure
+def test_fails_when_files_are_left_from_other_backend(
+    monkeypatch: pytest.MonkeyPatch,
+    temporary_home: Path,
+    sops_setup: SopsSetup,
+) -> None:
+    config = nested_dict()
+    my_secret_generator = config["clan"]["core"]["vars"]["generators"][
+        "my_secret_generator"
+    ]
+    my_secret_generator["files"]["my_secret"]["secret"] = True
+    my_secret_generator["script"] = "echo hello > $out/my_secret"
+    my_value_generator = config["clan"]["core"]["vars"]["generators"][
+        "my_value_generator"
+    ]
+    my_value_generator["files"]["my_value"]["secret"] = False
+    my_value_generator["script"] = "echo hello > $out/my_value"
+    flake = generate_flake(
+        temporary_home,
+        flake_template=CLAN_CORE / "templates" / "minimal",
+        machine_configs={"my_machine": config},
+        monkeypatch=monkeypatch,
+    )
+    sops_setup.init()
+    monkeypatch.chdir(flake.path)
+    for generator in ["my_secret_generator", "my_value_generator"]:
+        generate_vars_for_machine(
+            Machine(name="my_machine", flake=FlakeId(str(flake.path))),
+            generator,
+            regenerate=False,
+        )
+    my_secret_generator["files"]["my_secret"]["secret"] = False
+    my_value_generator["files"]["my_value"]["secret"] = True
+    set_machine_settings(flake.path, "my_machine", config)
+    monkeypatch.chdir(flake.path)
+    for generator in ["my_secret_generator", "my_value_generator"]:
+        with pytest.raises(ClanError):
+            generate_vars_for_machine(
+                Machine(name="my_machine", flake=FlakeId(str(flake.path))),
+                generator,
+                regenerate=False,
+            )
diff --git a/pkgs/clan-cli/tests/test_vars_deployment.py b/pkgs/clan-cli/tests/test_vars_deployment.py
index 69c294a28..7164e5e06 100644
--- a/pkgs/clan-cli/tests/test_vars_deployment.py
+++ b/pkgs/clan-cli/tests/test_vars_deployment.py
@@ -24,6 +24,9 @@ def test_vm_deployment(
     machine1_config["services"]["getty"]["autologinUser"] = "root"
     machine1_config["services"]["openssh"]["enable"] = True
     machine1_config["networking"]["firewall"]["enable"] = False
+    machine1_config["users"]["users"]["root"]["openssh"]["authorizedKeys"]["keys"] = [
+        # put your key here when debugging and pass ssh_port in run_vm_in_thread call below
+    ]
     m1_generator = machine1_config["clan"]["core"]["vars"]["generators"]["m1_generator"]
     m1_generator["files"]["my_secret"]["secret"] = True
     m1_generator["script"] = """
@@ -46,7 +49,7 @@ def test_vm_deployment(
     machine2_config["services"]["getty"]["autologinUser"] = "root"
     machine2_config["services"]["openssh"]["enable"] = True
     machine2_config["users"]["users"]["root"]["openssh"]["authorizedKeys"]["keys"] = [
-        "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIDuhpzDHBPvn8nv8RH1MRomDOaXyP4GziQm7r3MZ1Syk grmpf"
+        # put your key here when debugging and pass ssh_port in run_vm_in_thread call below
     ]
     machine2_config["networking"]["firewall"]["enable"] = False
     machine2_config["clan"]["core"]["vars"]["generators"]["my_shared_generator"] = (
@@ -94,7 +97,7 @@ def test_vm_deployment(
     # run nix flake lock
     cmd.run(["nix", "flake", "lock"])
     vm_m1 = run_vm_in_thread("m1_machine")
-    vm_m2 = run_vm_in_thread("m2_machine", ssh_port=2222)
+    vm_m2 = run_vm_in_thread("m2_machine")
     qga_m1 = qga_connect("m1_machine", vm_m1)
     qga_m2 = qga_connect("m2_machine", vm_m2)
     # check my_secret is deployed