diff --git a/src/cleveragents/cli/commands/plan.py b/src/cleveragents/cli/commands/plan.py
index cda1461fa..a88b9ebcf 100644
--- a/src/cleveragents/cli/commands/plan.py
+++ b/src/cleveragents/cli/commands/plan.py
@@ -583,7 +583,9 @@ def _cleanup_sandbox_for_plan(
             ):
                 continue
 
-            GitWorktreeSandbox.cleanup_stale(resource.location, plan_id)
+            GitWorktreeSandbox.cleanup_stale(
+                resource.location, plan_id, allow_destroy_with_changes=True
+            )
 
 
 class _SandboxInfo:
diff --git a/src/cleveragents/infrastructure/sandbox/git_worktree.py b/src/cleveragents/infrastructure/sandbox/git_worktree.py
index 3974679b8..b59cbb7d1 100644
--- a/src/cleveragents/infrastructure/sandbox/git_worktree.py
+++ b/src/cleveragents/infrastructure/sandbox/git_worktree.py
@@ -164,17 +164,37 @@ class GitWorktreeSandbox:
         """Context after creation, ``None`` before ``create``."""
         return self._context
 
-    # -- class helpers -------------------------------------------------------
+   # -- class helpers -------------------------------------------------------
 
     @classmethod
-    def cleanup_stale(cls, repo_path: str, plan_id: str) -> bool:
+    def cleanup_stale(
+        cls,
+        repo_path: str,
+        plan_id: str,
+        allow_destroy_with_changes: bool = False,
+    ) -> bool:
         """Remove a stale worktree branch left by a previous execution.
 
-        Idempotent — does nothing if no stale branch exists.
+        Idempotent -- does nothing if no stale branch exists.
+
+        When *allow_destroy_with_changes* is ``False`` (the default), the
+        method inspects the branch's diff against HEAD.  Branches with
+        insertions or modifications are preserved because they may contain
+        work waiting for **plan apply** to merge.  Only truly empty or
+        deletions-only branches are treated as stale and cleaned up.
+
+        When *allow_destroy_with_changes* is ``True`` (used by explicit
+        plan cancel), the old behaviour applies: any existing branch is
+        unconditionally destroyed regardless of whether it has changes.
 
         Args:
             repo_path: Absolute path to the git repository root.
             plan_id: The plan ULID whose stale branch should be removed.
+            allow_destroy_with_changes: If ``True``, always destroy the
+                branch even if it contains meaningful changes.  When
+                ``False`` (default), preserve branches with pending
+                insertions or modifications so that *plan apply* can
+                find the artifacts.
 
         Returns:
             ``True`` if a stale branch was found and cleaned up,
@@ -190,6 +210,54 @@ class GitWorktreeSandbox:
         except (subprocess.CalledProcessError, subprocess.TimeoutExpired):
             return False
 
+        # When not explicitly allowed to destroy with changes, inspect the
+        # branch diff before tearing it down.  Branches that have pending
+        # modifications are work products waiting for plan apply to merge;
+        # destroying them causes "plan apply" to find zero artifacts.
+        if not allow_destroy_with_changes:
+            try:
+                diff_result = _run_git(
+                    ["diff", "--shortstat", f"HEAD...{branch_name}"],
+                    cwd=repo_path,
+                )
+            except (subprocess.CalledProcessError, subprocess.TimeoutExpired):
+                # On inspection failure preserve the branch to avoid data loss
+                logger.debug(
+                    "Preserving sandbox branch due to diff check failure: branch=%s",
+                    branch_name,
+                )
+                return False
+
+            diff_text = diff_result.stdout.strip()
+            has_changes = bool(diff_text) and any(
+                keyword in diff_text
+                for keyword in ("insertion", "deletion")
+            )
+            # Also treat empty diffs (no files changed at all) as preserved.
+            if not diff_text:
+                has_changes = False
+
+            if has_changes:
+                logger.info(
+                    "Preserving sandbox branch with pending changes "
+                    "(plan apply has work to merge): branch=%s",
+                    branch_name,
+                )
+                return False
+
+            # Branch has only deletions or is empty - safe to clean up.
+            logger.info(
+                "Branch %s has no new insertions; treating as truly stale.",
+                branch_name,
+            )
+        else:
+            logger.info(
+                "Cleaning up sandbox branch (allow_destroy_with_changes): "
+                "branch=%s repo=%s",
+                branch_name,
+                repo_path,
+            )
+
         logger.info(
             "Cleaning up stale sandbox branch: branch=%s repo=%s",
             branch_name,