diff --git a/scripts/lib/CIME/case_submit.py b/scripts/lib/CIME/case_submit.py
index b5bd61de3fa..d10032e56d7 100644
--- a/scripts/lib/CIME/case_submit.py
+++ b/scripts/lib/CIME/case_submit.py
@@ -71,9 +71,13 @@ def submit(case, job=None, resubmit=False, no_batch=False, batch_args=None):
         casebaseid = case.get_value("CASEBASEID")
         # This should take care of the race condition where the submitted job
         # begins immediately and tries to set RUN phase. We proactively assume
-        # a passed SUBMIT phase.
+        # a passed SUBMIT phase. If this state is already PASS, don't set it again
+        # because then we'll lose RUN phase info if it's there. This info is important
+        # for system_tests_common to know if it needs to reinitialize the test or not.
         with TestStatus(test_dir=caseroot, test_name=casebaseid) as ts:
-            ts.set_status(SUBMIT_PHASE, TEST_PASS_STATUS)
+            phase_status = ts.get_status(SUBMIT_PHASE)
+            if phase_status != TEST_PASS_STATUS:
+                ts.set_status(SUBMIT_PHASE, TEST_PASS_STATUS)
 
     try:
         functor = lambda: _submit(case, job, resubmit, no_batch, batch_args)
diff --git a/scripts/lib/CIME/test_scheduler.py b/scripts/lib/CIME/test_scheduler.py
index f9bcdeb336a..0915df9c202 100644
--- a/scripts/lib/CIME/test_scheduler.py
+++ b/scripts/lib/CIME/test_scheduler.py
@@ -737,6 +737,8 @@ def _setup_cs_files(self):
             template = template.replace("<PATH>",
                                         os.path.join(self._cime_root,"scripts","Tools")).replace\
                                         ("<TESTID>", self._test_id)
+            if not os.path.exists(self._test_root):
+                os.makedirs(self._test_root)
             cs_status_file = os.path.join(self._test_root, "cs.status.%s" % self._test_id)
             with open(cs_status_file, "w") as fd:
                 fd.write(template)