diff --git a/pkgs/clan-cli/clan_cli/flake.py b/pkgs/clan-cli/clan_cli/flake.py
index 7a9aff8b6..3f3e40fdc 100644
--- a/pkgs/clan-cli/clan_cli/flake.py
+++ b/pkgs/clan-cli/clan_cli/flake.py
@@ -480,4 +480,38 @@ class Flake:
         if not self._cache.is_cached(selector):
             log.info(f"Cache miss for {selector}")
             self.get_from_nix([selector], nix_options)
-        return self._cache.select(selector)
+        value = self._cache.select(selector)
+
+        num_loops = 0
+
+        # Check if all nix store paths exist
+        # FIXME: If the value is a highly nested structure, this will be slow
+        def recursive_path_exists_check(val: Any) -> Any:
+            nonlocal num_loops
+            if isinstance(val, str):
+                if val.startswith("/nix/store/"):
+                    path = Path(val)
+                    if not path.exists():
+                        msg = f"{path} does not exist"
+                        raise ClanError(msg)
+
+            elif isinstance(val, dict):
+                return {k: recursive_path_exists_check(v) for k, v in val.items()}
+            elif isinstance(val, list):
+                return [recursive_path_exists_check(v) for v in val]
+            if num_loops > 75:
+                msg = "Maximum recursion depth (75) exceeded while checking paths"
+                log.warning(msg)
+                raise ClanError(msg)
+            num_loops += 1
+            return val
+
+        # If there are any paths that don't exist, refresh from nix
+        try:
+            recursive_path_exists_check(value)
+        except ClanError as e:
+            log.info(f"Path {e} for {selector} does not exist, refreshing from nix")
+            self.get_from_nix([selector], nix_options)
+            value = self._cache.select(selector)
+
+        return value