@Stateless
public class CommandA {
    
    public void execute(UUID userId) {
        final List resultList = entityManager.createQuery("select * from tableA where userId= ?1").setParameter(1, userId).getResultList();
        if (resultList.isEmpty()) {
            User user = new User();
            user.setUserId(userId)
            user.setValueA(...)
            entityManager.persist(user);  // <--- CREATES FIRST INSERT
        } else {
            resultList.get(0).setValueA(...);
            entityManager.merge(user);
        }
    }
    
}

@Stateless
public class CommandB  {

    public void execute(UUID userId) {
        final List resultList = entityManager.createNativeQuery("select * from tableA where userId = ?1").setParameter(1, userId).getResultList();
        if (resultList.isEmpty()) {
            User user = new User();
            user.setUserId(userId)
            user.setValueB(...)
            entityManager.persist(user);   // <-- CREATES second insert statement
        } else {
            resultList.get(0).setValueB(...);
            entityManager.merge(user);
        }
    }

}

@Stateless
public class OverallProcess {

    @EJB
    CommandA commandA;

    @EJB
    CommandB commandB;

    public void startingPoint() {
        commandA.execute(...);
        commandB.execute(...);
    }
    // --> after finishing this method (and the transaction is committed, it throws the exception because of unique constraint)
}