diff --git a/server/mergin/sync/public_api_v2_controller.py b/server/mergin/sync/public_api_v2_controller.py
index ec3fd260..e503edad 100644
--- a/server/mergin/sync/public_api_v2_controller.py
+++ b/server/mergin/sync/public_api_v2_controller.py
@@ -289,9 +289,11 @@ def create_project_version(id):
         db.session.add(pv)
         db.session.add(project)
         db.session.commit()
+
         # let's move uploaded files where they are expected to be
-        temp_files_dir = os.path.join(upload.upload_dir, "files", v_next_version)
-        os.renames(temp_files_dir, version_dir)
+        if to_be_added_files or to_be_updated_files:
+            temp_files_dir = os.path.join(upload.upload_dir, "files", v_next_version)
+            os.renames(temp_files_dir, version_dir)
 
         logging.info(
             f"Push finished for project: {project.id}, project version: {v_next_version}, upload id: {upload.id}."
diff --git a/server/mergin/tests/test_public_api_v2.py b/server/mergin/tests/test_public_api_v2.py
index 68df0949..1d5e0d7c 100644
--- a/server/mergin/tests/test_public_api_v2.py
+++ b/server/mergin/tests/test_public_api_v2.py
@@ -174,6 +174,21 @@ def test_project_members(client):
         204,
         None,
     ),
+    # only delete files
+    (
+        {
+            "version": "v1",
+            "changes": {
+                "added": [],
+                "removed": [
+                    file_info(test_project_dir, "base.gpkg"),
+                ],
+                "updated": [],
+            },
+        },
+        201,
+        None,
+    ),
     # broken .gpkg file
     (
         {"version": "v1", "changes": _get_changes_with_diff_0_size(test_project_dir)},