diff --git a/checker/tests/stubparser-nullness/NoExplicitAnnotations.java b/checker/tests/stubparser-nullness/NoExplicitAnnotations.java
index 82e72708ca5..5e0dd3d4062 100644
--- a/checker/tests/stubparser-nullness/NoExplicitAnnotations.java
+++ b/checker/tests/stubparser-nullness/NoExplicitAnnotations.java
@@ -51,6 +51,7 @@ void use(
             NoExplicitAnnotationsSub2 sub2,
             NoExplicitAnnotationsSub3 sub3) {
         nble = sub1.method1();
+        // :: error: (assignment.type.incompatible)
         nn = sub1.method1();
         nble = sub2.method2();
         nn = sub2.method2();
diff --git a/framework/src/main/java/org/checkerframework/framework/stub/AnnotationFileParser.java b/framework/src/main/java/org/checkerframework/framework/stub/AnnotationFileParser.java
index 0557b75cb6f..ef20f024d6e 100644
--- a/framework/src/main/java/org/checkerframework/framework/stub/AnnotationFileParser.java
+++ b/framework/src/main/java/org/checkerframework/framework/stub/AnnotationFileParser.java
@@ -1521,7 +1521,9 @@ private void clearAnnotations(AnnotatedTypeMirror atype, Type typeDef) {
         */
         // Clear existing annotations, which only makes a difference for
         // type variables, but doesn't hurt in other cases.
-        atype.clearAnnotations();
+        if (atype.getKind() == TypeKind.TYPEVAR) {
+            atype.clearAnnotations();
+        }
     }
 
     /**