diff --git a/doc/changes/DM-54613.other.rst b/doc/changes/DM-54613.other.rst
new file mode 100644
index 00000000..9e45c6ac
--- /dev/null
+++ b/doc/changes/DM-54613.other.rst
@@ -0,0 +1,2 @@
+Changed BPS behavior so it doesn't throw when there are job labels in job ordering groups that were not included in the final version of the workflow.
+From now on BPS will only warn the user when it occures.
diff --git a/python/lsst/ctrl/bps/generic_workflow.py b/python/lsst/ctrl/bps/generic_workflow.py
index 65889d95..c3c583bc 100644
--- a/python/lsst/ctrl/bps/generic_workflow.py
+++ b/python/lsst/ctrl/bps/generic_workflow.py
@@ -990,9 +990,10 @@ def _check_job_ordering_config(self, ordering_config: dict[str, Any]) -> dict[st
 
             if unused_labels:
                 _LOG.info("Workflow job labels = %s", ",".join(self._job_labels.labels))
-                raise RuntimeError(
-                    f"Job label(s) ({','.join(unused_labels)}) from job ordering group "
-                    f"{group} does not exist in workflow.  Aborting."
+                _LOG.warning(
+                    "Job label(s) (%s) from job ordering group %s does not exist in workflow.",
+                    ",".join(unused_labels),
+                    group,
                 )
 
             label_subgraph = self._job_labels.subgraph(job_labels)
diff --git a/tests/test_generic_workflow.py b/tests/test_generic_workflow.py
index 13cb37e2..a48f951e 100644
--- a/tests/test_generic_workflow.py
+++ b/tests/test_generic_workflow.py
@@ -451,11 +451,7 @@ def testCheckJobOrderingConfigBadLabel(self):
 
     def testCheckJobOrderingConfigUnusedLabel(self):
         gwf = gtu.make_3_label_workflow("test_unused_label", final=True)
-        with self.assertRaisesRegex(
-            RuntimeError,
-            r"Job label\(s\) \(unused1,unused2\) from job ordering group "
-            "order1 does not exist in workflow.  Aborting.",
-        ):
+        with self.assertLogs("lsst.ctrl.bps.generic_workflow", level=logging.WARNING) as cm:
             gwf._check_job_ordering_config(
                 {
                     "order1": {
@@ -465,6 +461,14 @@ def testCheckJobOrderingConfigUnusedLabel(self):
                     },
                 }
             )
+        self.assertTrue(
+            any(
+                "Job label(s) (unused1,unused2) from job ordering group order1 does not exist in workflow."
+                in record.getMessage()
+                for record in cm.records
+            ),
+            "Expected warning about unused labels",
+        )
 
     def testCheckJobOrderingConfigMissingDim(self):
         gwf = gtu.make_3_label_workflow("test_missing_dim", final=True)