We resolved this issue by creating the query with toplinks api:
ReadAllQuery raq = new ReadAllQuery(TopLevel.class);
ExpressionBuilder eb = raq.getExpressionBuilder();
Expression level1 = eb.anyOf("level1List");
raq.addJoinedAttribute(level1);
Expression level2 = level1.anyOf("level2List");
raq.addJoinedAttribute(level2);
Expression level3 = level2.anyOf("level3List");
raq.addJoinedAttribute(level3);
Expression level4 = level3.anyOf("level4List");
raq.addJoinedAttribute(level4);
Query jpaQuery = new EJBQueryImpl(raq, (EntityManagerImpl)em.getDelegate());
TopLevel tl = (TopLevel) jpaQuery.getSingleResult();
return tl;
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