diff --git a/src/main/java/org/checkerframework/specimin/SpeciminRunner.java b/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
index 5b434410..3a77c32c 100644
--- a/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
+++ b/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
@@ -502,10 +502,20 @@ private static void performMinimizationImpl(
 
     // cache to avoid called Files.createDirectories repeatedly with the same arguments
     Set<Path> createdDirectories = new HashSet<>();
+    Set<String> targetFilesAbsolutePaths = new HashSet<>();
+
+    for (String target : targetFiles) {
+      File targetFile = new File(target);
+      // Convert to absolute path for comparison
+      targetFilesAbsolutePaths.add(targetFile.getAbsolutePath());
+    }
 
     for (Entry<String, CompilationUnit> target : parsedTargetFiles.entrySet()) {
-      // ignore classes from the Java package.
-      if (target.getKey().startsWith("java/")) {
+      // ignore classes from the Java package, unless we are targeting a JDK file.
+      // However, all related java/ files should not be included (as in used, but not targeted)
+      String absolutePath = new File(target.getKey()).getAbsolutePath();
+      if (!targetFilesAbsolutePaths.contains(absolutePath)
+          && (target.getKey().startsWith("java/") || target.getKey().startsWith("java\\"))) {
         continue;
       }
       // If a compilation output's entire body has been removed and the related class is not used by
diff --git a/src/main/resources/preservation_status.json b/src/main/resources/preservation_status.json
index d4d7c3c5..6274ea26 100644
--- a/src/main/resources/preservation_status.json
+++ b/src/main/resources/preservation_status.json
@@ -20,7 +20,7 @@
   "jdk-8319461": "PASS",
   "jdk-8288590": "PASS",
   "na-89": "FAIL",
-  "na-97": "FAIL",
+  "na-97": "PASS",
   "na-102": "PASS",
   "na-103": "PASS",
   "na-176": "FAIL",