diff --git a/snakecnv/mergebatches.snk b/snakecnv/mergebatches.snk
index 16a8331000c67865756f267c927fb51d9f32a9e2..052e5e3fe99930cba6e12e11e4a9f42a9aefa3f8 100644
--- a/snakecnv/mergebatches.snk
+++ b/snakecnv/mergebatches.snk
@@ -87,8 +87,9 @@ batches, chromosomes, variant_types = get_batches(WDIR)
 if len(batches) == 1:
     b_filtered = os.path.join(WDIR, "batch001", "filtered")
     f_filtered = os.path.join(WDIR, "filtered")
-    shutil.move(b_filtered, f_filtered)
-    os.symlink(f_filtered, b_filtered)
+    if not os.path.exists(f_filtered):
+        shutil.move(b_filtered, f_filtered)
+        os.symlink(f_filtered, b_filtered)
 
 include: "tools/threads.snk"