The following example involves an annotation that transitively references a missing enum class file, annotation processing, and javac's native header support (-h). The missing class file does not cause the compilation to fail, and instead results in an incorrect native header file being produced.

I tested with JDK 10-ea+37.

Repro:

=== ./A.java
@B(E.FOO)
@interface A {}
=== ./B.java
@interface B {
  E value() default E.FOO;
}
=== ./E.java
public enum E {
  FOO
}
=== ./T.java
@A
class T {
  public static native void f(int i, long l, String s);
}
=== ./P.java
import java.util.Set;
import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.TypeElement;

@SupportedAnnotationTypes("*")
public final class P extends AbstractProcessor {

  @Override
  public SourceVersion getSupportedSourceVersion() {
    return SourceVersion.latestSupported();
  }

  @Override
  public final boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
    return true;
  }
}
===

Note that the header for T.f changes after the class for for E is removed from the classpath:

$ javac -fullversion
javac full version "10-ea+37"
$ javac A.java B.java E.java P.java
$ javac -processor P -implicit:none -sourcepath : -h h T.java && grep -A 1 Java_T_f h/T.h
...
JNIEXPORT void JNICALL Java_T_f
  (JNIEnv *, jclass, jint, jlong, jstring);

$ rm E.class
$ javac -processor P -implicit:none -sourcepath : -h h T.java && grep -A 1 Java_T_f h/T.h
...
warning: unknown enum constant E.FOO
  reason: class file for E not found
...
JNIEXPORT void JNICALL Java_T_f
  (JNIEnv *, jclass, jint, jlong, jobject);