diff --git a/sjsonnet/test/resources/refresh_golden_outputs.sh b/sjsonnet/test/resources/refresh_golden_outputs.sh
index 002e308c..29da81a8 100755
--- a/sjsonnet/test/resources/refresh_golden_outputs.sh
+++ b/sjsonnet/test/resources/refresh_golden_outputs.sh
@@ -28,6 +28,8 @@ if [ $# -gt 0 ]; then
     fi
 
     java $JAVA_OPTS -jar "$SJSONNET" $PARAMS $EXT_PARAMS $TLA_PARAMS "$f" > "$f.golden" 2>&1 || true
+    # Strip Java runtime WARNING lines (e.g. sun.misc.Unsafe deprecation)
+    sed -i '' '/^WARNING:/d' "$f.golden"
   done
   popd || exit 1
   echo "Done refreshing specified golden outputs."
@@ -52,6 +54,8 @@ for f in *.jsonnet; do
   fi
 
   java $JAVA_OPTS -jar "$SJSONNET" $PARAMS $EXT_PARAMS $TLA_PARAMS "$f" > "$f.golden" 2>&1 || true
+  # Strip Java runtime WARNING lines (e.g. sun.misc.Unsafe deprecation)
+  sed -i '' '/^WARNING:/d' "$f.golden"
 done
 popd || exit 1
 
@@ -64,6 +68,8 @@ for f in *.jsonnet; do
 
   echo "  Processing file: $f"
   java $JAVA_OPTS -jar "$SJSONNET" $PARAMS "$f" > "$f.golden" 2>&1 || true
+  # Strip Java runtime WARNING lines (e.g. sun.misc.Unsafe deprecation)
+  sed -i '' '/^WARNING:/d' "$f.golden"
 done
 popd || exit 1
 
@@ -76,6 +82,8 @@ for f in *.jsonnet; do
 
   echo "  Processing file: $f"
   java $JAVA_OPTS -jar "$SJSONNET" $PARAMS "$f" > "$f.golden" 2>&1 || true
+  # Strip Java runtime WARNING lines (e.g. sun.misc.Unsafe deprecation)
+  sed -i '' '/^WARNING:/d' "$f.golden"
 done
 popd || exit 1
 
diff --git a/sync_test_suites.sh b/sync_test_suites.sh
index 9efd330b..f1fa36e4 100755
--- a/sync_test_suites.sh
+++ b/sync_test_suites.sh
@@ -242,6 +242,13 @@ sync_test_files() {
     if [ ! -e "$dest_file" ]; then
       cp -r "$src_file" "$dest_file"
       new_golden=$((new_golden + 1))
+      # If the new golden is an error output, regenerate with sjsonnet's error format
+      if ! is_success_golden "$src_file"; then
+        local jsonnet_file="$target_dir/${stem}.jsonnet"
+        if [ -f "$jsonnet_file" ]; then
+          echo "$jsonnet_file" >> "$GOLDEN_REFRESH_FILES"
+        fi
+      fi
     elif ! diff -q "$src_file" "$dest_file" > /dev/null 2>&1; then
       local src_ok=0 dest_ok=0
       is_success_golden "$src_file" && src_ok=1
@@ -301,6 +308,13 @@ sync_test_files() {
       if [ ! -e "$dest_file" ]; then
         cp -r "$src_entry" "$dest_file"
         new_golden=$((new_golden + 1))
+        # If the new golden is an error output, regenerate with sjsonnet's error format
+        if ! is_success_golden "$src_entry"; then
+          local local_jsonnet="$target_dir/${stem}.jsonnet"
+          if [ -f "$local_jsonnet" ]; then
+            echo "$local_jsonnet" >> "$GOLDEN_REFRESH_FILES"
+          fi
+        fi
       elif ! diff -q "$src_entry" "$dest_file" > /dev/null 2>&1; then
         local src_ok=0 dest_ok=0
         is_success_golden "$src_entry" && src_ok=1