diff --git a/src/compiler/nir/nir_linking_helpers.c b/src/compiler/nir/nir_linking_helpers.c
index 8874540b73b..9ed249e94d9 100644
--- a/src/compiler/nir/nir_linking_helpers.c
+++ b/src/compiler/nir/nir_linking_helpers.c
@@ -1074,6 +1074,9 @@ replace_varying_input_by_constant_load(nir_shader *shader,
       }
    }
 
+   if (progress)
+      nir_metadata_preserve(impl, nir_metadata_control_flow);
+
    return progress;
 }
 
@@ -1120,6 +1123,9 @@ replace_duplicate_input(nir_shader *shader, nir_variable *input_var,
       }
    }
 
+   if (progress)
+      nir_metadata_preserve(impl, nir_metadata_control_flow);
+
    return progress;
 }
 
@@ -1285,6 +1291,9 @@ replace_varying_input_by_uniform_load(nir_shader *shader,
       }
    }
 
+   if (progress)
+      nir_metadata_preserve(impl, nir_metadata_control_flow);
+
    return progress;
 }