diff --git a/tools/testing/ktest/ktest.pl b/tools/testing/ktest/ktest.pl
index 223d88e25e05..74b4455c8839 100755
--- a/tools/testing/ktest/ktest.pl
+++ b/tools/testing/ktest/ktest.pl
@@ -3751,9 +3751,10 @@ sub test_this_config {
     # .config to make sure it is missing the config that
     # we had before
     my %configs = %min_configs;
-    delete $configs{$config};
+    $configs{$config} = "# $config is not set";
     make_new_config ((values %configs), (values %keep_configs));
     make_oldconfig;
+    delete $configs{$config};
     undef %configs;
     assign_configs \%configs, $output_config;