doctrine of Estoppel in service matters

an existing rule prescribes a different pattern of Marks for promotion by selection but the Department is following some other pattern than what is prescribed. When this was questioned, The department issues an amendment to the rule and further, the amendment was made applicable retrospectively by another amendment at a subsequent date. When the matter is put before the court, the Department takes the defense of Estoppel, saying that the applicant before the tribunnal, has unsuccessfully appeared in the selection and is thus estopped from claiming improper application of rules on the date of selection. But the question raised was that the amendment so issued was against Article 14 of the constitution where class classification with intelligible differentia is permitted and this amendment is affecting the applicant and other equally placed employees, which the forum failed to appreciate and has applied Estoppel.
Please advise me whether this is a fit case to be contested before the higher judiciary and also when an authority has not followed the prescribed rule is it not mandatory for that authority to follow that rule instead of taking shelter under estoppel. Please comment and advise.