diff --git a/vndk/tools/header-checker/src/diff/abi_diff.cpp b/vndk/tools/header-checker/src/diff/abi_diff.cpp
index 8a2ccf9d2..cfd559c07 100644
--- a/vndk/tools/header-checker/src/diff/abi_diff.cpp
+++ b/vndk/tools/header-checker/src/diff/abi_diff.cpp
@@ -382,8 +382,11 @@ bool HeaderAbiDiff::DumpDiffElements(
     const T *old_element = pair.first;
     const T *new_element = pair.second;
 
+    // The old and new linker set keys are supposed to be equal.
     if (IgnoreSymbol<T>(old_element, ignored_symbols_,
-                        [](const T *e) {return e->GetLinkerSetKey();})) {
+                        [](const T *e) { return e->GetLinkerSetKey(); }) ||
+        ignored_linker_set_keys_.find(old_element->GetLinkerSetKey()) !=
+            ignored_linker_set_keys_.end()) {
       continue;
     }
 
diff --git a/vndk/tools/header-checker/src/diff/abi_diff_wrappers.cpp b/vndk/tools/header-checker/src/diff/abi_diff_wrappers.cpp
index 87ac0fe6d..0b2d0b1ac 100644
--- a/vndk/tools/header-checker/src/diff/abi_diff_wrappers.cpp
+++ b/vndk/tools/header-checker/src/diff/abi_diff_wrappers.cpp
@@ -32,10 +32,6 @@ template <>
 bool DiffWrapper<repr::RecordTypeIR>::DumpDiff(
     repr::DiffMessageIR::DiffKind diff_kind) {
   std::deque<std::string> type_queue;
-  if (oldp_->GetLinkerSetKey() != newp_->GetLinkerSetKey()) {
-    llvm::errs() << "Comparing two different unreferenced records\n";
-    return false;
-  }
   if (!type_cache_->insert(
           oldp_->GetSelfType() + newp_->GetSelfType()).second) {
     return true;
@@ -48,10 +44,6 @@ template <>
 bool DiffWrapper<repr::EnumTypeIR>::DumpDiff(
     repr::DiffMessageIR::DiffKind diff_kind) {
   std::deque<std::string> type_queue;
-  if (oldp_->GetLinkerSetKey() != newp_->GetLinkerSetKey()) {
-    llvm::errs() << "Comparing two different unreferenced enums\n";
-    return false;
-  }
   if (!type_cache_->insert(
       oldp_->GetSelfType() + newp_->GetSelfType()).second) {
     return true;
diff --git a/vndk/tools/header-checker/tests/test.py b/vndk/tools/header-checker/tests/test.py
index 7c0f43c7f..fd9a93153 100755
--- a/vndk/tools/header-checker/tests/test.py
+++ b/vndk/tools/header-checker/tests/test.py
@@ -178,6 +178,10 @@ class HeaderCheckerTest(unittest.TestCase):
     def test_libgolden_cpp_return_type_diff(self):
         self.prepare_and_run_abi_diff_all_archs(
             "libgolden_cpp", "libgolden_cpp_return_type_diff", 8)
+        self.prepare_and_run_abi_diff_all_archs(
+            "libgolden_cpp", "libgolden_cpp_return_type_diff", 0,
+            ["-ignore-linker-set-key", "_ZN17HighVolumeSpeaker6ListenEv",
+             "-ignore-linker-set-key", "_ZN16LowVolumeSpeaker6ListenEv"])
 
     def test_libgolden_cpp_add_odr(self):
         self.prepare_and_run_abi_diff_all_archs(