If a person omits a Waajib of Salaah due to error then the error can be rectified by performing Sajda-e-Sahw. However, if a Waajib of Salaah is omitted intentionally then one will be required to repeat the entire Salaah and even Sajda-e-Sahw will not suffice in this particular instance. However, the Salaah should be repeated within the time (of that particular Salaah). Once the duration of that particular Salaah elapses, the need of repeating the Salaah no longer remains and the Salaah performed in a deficient or incomplete manner will absolve one of his duty.
In our scenario, the Witr Salaah performed for a period of 5 years without recitation of the Qunoot will not have to be repeated since the time of the Salaah has elapsed and the Salaah will be considered to be discharged albeit in a deficient manner.