diff --git a/scripts/install.ps1 b/scripts/install.ps1
index 4706778cc95..3965435c1c1 100644
--- a/scripts/install.ps1
+++ b/scripts/install.ps1
@@ -1209,16 +1209,19 @@ function Install-Repository {
             }
             $didUpdate = $true
         } else {
-            # Directory exists but isn't a usable git repo.  Wipe it and
-            # fall through to a fresh clone.  A leftover ``.git`` stub from
-            # a partial uninstall used to lock the installer into the
-            # "update" branch forever, emitting three ``fatal: not a git
-            # repository`` errors and failing with "not in a git directory".
-            Write-Warn "Existing directory at $InstallDir is not a valid git repo -- replacing it."
+            # Directory exists but isn't a usable git repo -- e.g. an
+            # interrupted clone with no initial commit (#40998), or a leftover
+            # ``.git`` stub from a partial uninstall that used to lock the
+            # installer into the "update" branch forever. Move it aside rather
+            # than deleting it -- never destroy a directory the user might still
+            # want -- and fall through to a fresh clone.
+            $backupDir = "$InstallDir.broken-" + (Get-Date -Format "yyyyMMdd-HHmmss")
+            Write-Warn "Existing directory at $InstallDir is not a valid git repo."
+            Write-Warn "Moving it aside to $backupDir before re-cloning."
             try {
-                Remove-Item -Recurse -Force $InstallDir -ErrorAction Stop
+                Move-Item -LiteralPath $InstallDir -Destination $backupDir -ErrorAction Stop
             } catch {
-                Write-Err "Could not remove $InstallDir : $_"
+                Write-Err "Could not move $InstallDir aside : $_"
                 Write-Info "Close any programs that might be using files in $InstallDir (editors,"
                 Write-Info "terminals, running hermes processes) and try again."
                 throw
diff --git a/scripts/install.sh b/scripts/install.sh
index 05270254993..db3ae5b8bb6 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -1094,11 +1094,14 @@ clone_repo() {
 
     # An interrupted previous clone leaves a .git with no initial commit, where
     # the update path's `git stash` / `git checkout` abort with "You do not
-    # have the initial commit yet" and fail the install (#40998). Drop such a
-    # partial checkout so the fresh-clone path below handles it cleanly.
+    # have the initial commit yet" and fail the install (#40998). Move such a
+    # partial checkout aside -- never delete it, in case it holds something the
+    # user wants -- so the fresh-clone path below can proceed.
     if [ -d "$INSTALL_DIR/.git" ] && ! git -C "$INSTALL_DIR" rev-parse --verify HEAD >/dev/null 2>&1; then
-        log_warn "Existing checkout at $INSTALL_DIR has no commits (interrupted clone) -- replacing it."
-        rm -rf "$INSTALL_DIR"
+        backup_dir="${INSTALL_DIR}.broken-$(date -u +%Y%m%d-%H%M%S)"
+        log_warn "Existing checkout at $INSTALL_DIR has no commits (interrupted clone)."
+        log_warn "Moving it aside to $backup_dir before re-cloning."
+        mv "$INSTALL_DIR" "$backup_dir"
     fi
 
     if [ -d "$INSTALL_DIR" ]; then
diff --git a/tests/test_install_no_initial_commit.py b/tests/test_install_no_initial_commit.py
index 586f7b35cb0..321ddd0b400 100644
--- a/tests/test_install_no_initial_commit.py
+++ b/tests/test_install_no_initial_commit.py
@@ -64,7 +64,7 @@ def _run_guard(install_dir: Path) -> None:
     assert res.returncode == 0, res.stderr
 
 
-def test_install_sh_guard_removes_commitless_checkout(tmp_path: Path) -> None:
+def test_install_sh_guard_moves_commitless_checkout_aside(tmp_path: Path) -> None:
     install_dir = tmp_path / "hermes-agent"
     install_dir.mkdir()
     _git(install_dir, "init")
@@ -78,7 +78,12 @@ def test_install_sh_guard_removes_commitless_checkout(tmp_path: Path) -> None:
     assert head.returncode != 0
 
     _run_guard(install_dir)
-    assert not install_dir.exists(), "commit-less checkout should be removed"
+    # The original path is cleared so a fresh clone can proceed, but the
+    # content is preserved in a backup (never deleted -- review feedback).
+    assert not install_dir.exists(), "commit-less checkout should be moved aside"
+    backups = list(install_dir.parent.glob(install_dir.name + ".broken-*"))
+    assert len(backups) == 1, "broken checkout should be moved to one backup dir"
+    assert (backups[0] / "leftover.txt").read_text() == "partial download"
 
 
 def test_install_sh_guard_keeps_repo_with_commits(tmp_path: Path) -> None:
@@ -92,6 +97,9 @@ def test_install_sh_guard_keeps_repo_with_commits(tmp_path: Path) -> None:
     _run_guard(install_dir)
     assert install_dir.exists()
     assert (install_dir / "f.txt").exists(), "a real checkout must be left intact"
+    assert not list(install_dir.parent.glob(install_dir.name + ".broken-*")), (
+        "a healthy checkout must not be moved aside"
+    )
 
 
 def test_install_sh_guard_ignores_non_repo_dir(tmp_path: Path) -> None:
@@ -117,3 +125,12 @@ def test_install_ps1_validity_requires_initial_commit() -> None:
         r"if \(\$revParseOk -and \$statusOk -and \$hasCommit\) \{",
         text,
     ), "repo validity must be gated on $hasCommit, not just rev-parse + status"
+    # Cleanup must be non-destructive: move the broken checkout aside, never
+    # `Remove-Item -Recurse -Force` it (review feedback on #40998).
+    assert "Move-Item -LiteralPath $InstallDir" in text, (
+        "install.ps1 must move an invalid checkout aside, not delete it"
+    )
+    assert "Remove-Item -Recurse -Force $InstallDir -ErrorAction Stop" not in text, (
+        "the destructive wipe of an existing install dir must be gone "
+        "(transient cleanup of a just-failed clone is fine)"
+    )