diff --git a/src/specify_cli/extensions/__init__.py b/src/specify_cli/extensions/__init__.py
index 8dd1b10554..70ace6a777 100644
--- a/src/specify_cli/extensions/__init__.py
+++ b/src/specify_cli/extensions/__init__.py
@@ -1395,6 +1395,33 @@ def install_from_directory(
                 backup_config_dir.unlink()
             did_remove = self.remove(manifest.id)
 
+        # A prior `remove(keep_config=True)` leaves the top-level
+        # *-config.yml / *-config.local.yml in place while dropping the
+        # registry entry. A later reinstall is not a --force removal
+        # (did_remove is False), so the rmtree below would wipe those
+        # preserved configs and the backup-restore path never runs. Capture
+        # them here and write them back after the fresh copytree, mirroring
+        # the *-config filter the --force restore path uses.
+        # Capture (bytes, mode) so we can restore permissions too — config
+        # files may hold secrets (API keys), and recreating them with default
+        # perms could widen access. Mirrors the --force restore's shutil.copy2
+        # (which preserves mode/mtime).
+        preserved_configs: dict[str, tuple[bytes, int]] = {}
+        if dest_dir.exists():
+            for cfg_file in dest_dir.iterdir():
+                if (
+                    cfg_file.is_file()
+                    and not cfg_file.is_symlink()
+                    and (
+                        cfg_file.name.endswith("-config.yml")
+                        or cfg_file.name.endswith("-config.local.yml")
+                    )
+                ):
+                    preserved_configs[cfg_file.name] = (
+                        cfg_file.read_bytes(),
+                        cfg_file.stat().st_mode,
+                    )
+
         # Install extension (dest_dir computed above during self-install guard)
         if dest_dir.exists():
             shutil.rmtree(dest_dir)
@@ -1402,6 +1429,18 @@ def install_from_directory(
         ignore_fn = self._load_extensionignore(source_dir)
         shutil.copytree(source_dir, dest_dir, ignore=ignore_fn)
 
+        # Restore configs preserved from a keep-config leftover (see above),
+        # preserving the original file mode. The --force backup-restore below
+        # (did_remove) still takes precedence for that path, which uses
+        # .backup/ rather than an in-place leftover.
+        for name, (data, mode) in preserved_configs.items():
+            dest_cfg = dest_dir / name
+            dest_cfg.write_bytes(data)
+            try:
+                os.chmod(dest_cfg, mode & 0o7777)  # permission bits only
+            except OSError:
+                pass
+
         # Register commands with AI agents
         registered_commands = {}
         if register_commands:
diff --git a/tests/test_extensions.py b/tests/test_extensions.py
index 2a4b2aa660..44b5985033 100644
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -1553,6 +1553,35 @@ def test_config_backup_on_remove(self, extension_dir, project_dir):
         assert backup_file.exists()
         assert backup_file.read_text() == "test: config"
 
+    def test_reinstall_preserves_keep_config_leftover(self, extension_dir, project_dir):
+        """A reinstall after `remove(keep_config=True)` must not wipe the
+        preserved config. remove(keep_config=True) leaves the *-config.yml in
+        place and drops the registry entry; the subsequent reinstall is not a
+        --force removal, so the unconditional rmtree used to destroy it."""
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        ext_dir = project_dir / ".specify" / "extensions" / "test-ext"
+        config_file = ext_dir / "test-ext-config.yml"
+        config_file.write_text("api_key: MY-CUSTOMIZED-VALUE")
+        # Restrictive perms — a config may hold secrets; the restore must not
+        # widen them (POSIX only; Windows chmod ignores group/other bits).
+        config_file.chmod(0o600)
+
+        # keep-config removal: registry entry dropped, config left in place.
+        assert manager.remove("test-ext", keep_config=True) is True
+        assert config_file.exists()
+
+        # Reinstall (no --force; registry now reports not-installed).
+        manager.install_from_directory(extension_dir, "0.1.0", register_commands=False)
+
+        # The user's config must survive the reinstall (was silently wiped).
+        assert config_file.exists()
+        assert "MY-CUSTOMIZED-VALUE" in config_file.read_text()
+        # ...and keep its original (restrictive) mode, not default perms.
+        if platform.system() != "Windows":
+            assert config_file.stat().st_mode & 0o777 == 0o600
+
 
 # ===== CommandRegistrar Tests =====